diff --git a/CLAUDE.md b/CLAUDE.md index 51f365f..17afbc5 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -272,16 +272,17 @@ handles stock sequences and third-party ones are what force a manual rebuild. scan a person should look at, which is what that verdict means. No shipped example does it; the branch exists so a future one is visible rather than quietly resolved. -- The corpus stands at 469 third-party, 246 stock and 5 unrecognized, pinned by +- The corpus stands at 584 third-party, 272 stock and 21 unrecognized, pinned by `test_the_shipped_examples_are_accounted_for_apart_from_a_pinned_few`. `tse_crusher` (`Flair axial low SAR`) is labelled `USER` and so reports third-party; `fl3d_rd` (`vessels_head`) is labelled `SIEMENS` and is also in `stock_binaries`. The five unaccounted scans are all in `XA60-Potpourri`, added for the `.exar1` work rather than for sequence detection: Siemens kernels (`epfid`, `epse`, `fl`) carrying MGH's FLEET/ACS modifications, whose - extra parameters no signature claims. They are named individually rather than - counted, so a *sixth* unaccounted scan -- or one of these five quietly - resolving -- still fails. That test asserted zero before, and relaxing it was + extra parameters no signature claims. They recur in all three Potpourri + exports (P1, P1_changed, P2), so the pinned set is the product of five scan + names and three export names rather than fifteen literals -- a *sixth* + unaccounted scan, or one of these five quietly resolving, still fails. That test asserted zero before, and relaxing it was the deliberate act the previous wording called for; writing signatures to force it back to zero would mean attributing sequences from inference alone, which is exactly what the attribution rule above forbids. @@ -291,11 +292,14 @@ handles stock sequences and third-party ones are what force a manual rebuild. `siemens_protocol.exar` reads and rewrites the protocol archives XA exports. None of this is documented by Siemens; every claim below was established against real exports and is asserted in `tests/test_exar.py` rather than -assumed. The corpus is `examples/XA60/Potpourri.exar1` plus -`Potpourri_changed.exar1`, which is the same export re-saved after changing TR -on five scans -- a deliberate one-parameter probe, not a second real protocol. -`Potpourri.pdf` is that same tree's PDF export, which is what lets the two -readers be checked against each other. +assumed. The corpus is one protocol carried on two XA60 scanners: `Potpourri_P1` +and `Potpourri_P2`, each with its PDF export. Two re-saved variants are the +answer keys the mappings rest on: `Potpourri_P2_changed` moves TR alone on five +scans, and `Potpourri_P1_changed` moves many parameters across five scans +including the Special card, with its own PDF. Having the PDF beside the archive +is what lets the two readers be checked against each other, and having a +before/after pair is the only way to learn where a printed value is stored -- +`sWipMemBlock` in particular is unreadable without one. - **The format is five layers deep**: SQLite -> raw DEFLATE (`wbits=-15`, no zlib or gzip wrapper) -> a one-line `EDF V1: ContentType=...;` header -> a @@ -325,9 +329,12 @@ readers be checked against each other. sixteen bytes each. Reading them big-endian gives well-formed GUIDs that match no element, so the failure is an empty tree rather than an error. - **Scan names are not in the protocol.** They hang off `Instance.LabelElement_id` - on an `EdfString` node whose content is a locale table, `{"Texts": {"": name}}`, - with the empty key as default. That is deliberate: renaming a scan must not - re-hash the protocol. + on an `EdfString` node whose content is a locale table. That is deliberate: + renaming a scan must not re-hash the protocol. The key is not always the same + -- most archives use `""` for the default, but some write `"en"` with no empty + key at all, and both spellings are in the corpus. Reading only `""` yields a + nameless tree on those, which looks like a reader that cannot find the labels + rather than one looking under the wrong key. - **`Preview` is the bridge to the PDF.** Each protocol carries a flat map of `{Label, Unit, Value}` entries whose labels are the ones the PDF prints -- `TR`, `Slice Thickness`, `FOV Read`. It is a per-protocol dictionary from printed @@ -339,6 +346,62 @@ readers be checked against each other. Patch only the preview and the console lists a number the scan will not use; patch only the ASCCONV and the list goes stale. The console also recomputes derived values -- `lScanTimeSec` followed TR -- which a patcher does not. +- **"Two places" is the simple case; there are four shapes.** Some parameters + are an ASCCONV *array*: `FOV Read` and `Slice Thickness` are replicated across + every `sSliceArray.asSlice[]` element -- three on a localizer, sixty-four on a + multi-slice EPI -- and writing element zero alone yields a protocol that loads, + lists correctly and is wrong. Some are *derived*: `FOV Phase` is a percentage + on the card but millimetres in the protocol, `dPhaseFOV = dReadoutFOV * pct/100`. + Some are ASCCONV *only*: nothing on the Special card appears in `Preview` at + all, so those have no preview side to keep in sync. And `Preview` is the + console's listing, not a mirror of the printout -- a multi-echo scan prints + `TE 1`..`TE 4` and `Preview` carries only the first, the rest living in + `alTE[1..3]` alone. +- **`dThickness` is the slice on a 2D acquisition and the whole slab on a 3D + one.** `sKSpace.ucDimension` is 2 or 4 and decides which; on all eight 3D + protocols `dThickness` is exactly the displayed thickness times + `sKSpace.lImagesPerSlab`. Writing the displayed number straight in would put + 1.0 where the protocol holds 176.0. This was caught by the mapping test + re-deriving its evidence rather than trusting the table, which is the whole + reason that test exists. +- **`FOV Phase` cannot be reproduced exactly from a percentage.** The console + quantises it to a ratio the hardware can realise -- 29/30 of the read FOV, + printed as 96.7% -- so writing `read * 96.7/100` lands within a rounding of + the console's value but not on it. Assert to within the printed precision and + say so in the manifest; do not fudge the number to match. +- **`sWipMemBlock` has no global meaning, so its mappings are per sequence.** + It is scratch memory the sequence binary reads as it likes. `alFree[0]` is MT + Flip Angle on `can_neuromelanin` and a packed word of checkbox flags on CMRR's + multiband sequences; `alFree[1]` is Readout polarity on `tfl_mgh_epinav_ABCD` + and Protocol filename on `ep_moco_nav_set_ABCD`; `alFree[12]` is Nav. location + on the MPRAGE navigator and Include Nav. on the SPACE one. A table treating an + index as one parameter would write a flip angle into CMRR's flags, so anything + reaching into `sWipMemBlock` must name its sequences and a test enforces it. +- **The option-scan archives are what pin the Special card**, and nothing else + can. `CMRR_optionscan_P1`, `MEMPRAGE_optionscan_P1` and `NAV_optionscan_P1` + each hold one sequence repeated with a single option changed per copy -- 33, + 7 and 31 scans -- so diffing each against its group's baseline gives one + labelled change against one moved field. That yields three encodings: values + written directly, small-integer enums (`Averaging` is 1=None 2=Linear 3=RMS + 4=RMS only 5=Mean), and CMRR's fourteen-bit flags word in `alFree[0]`. + `tests/test_exar_patch.py` replays all 62 toggles through the patcher and + requires every one to reproduce the console. +- **`sWipMemBlock` arrays are sparse: an assignment holding zero is not + written at all.** A CMRR protocol with every Special-card box unticked has no + `alFree[0]` line, and setting `Remeasure` to zero deleted its line rather + than writing `0`. Elements are listed in ascending index order, so creating + one means inserting it among its siblings and not appending. A patcher that + only overwrites existing assignments cannot turn a first flag on, which is + how this was found. +- **A flags word carries bits no mapping claims.** Comparing a whole `alFree[0]` + against the console's is therefore wrong; compare the bit a mapping claims. + The Potpourri edit toggled `Echoes in separate series`, which no option scan + has pinned, and it shares the word with fourteen options that are pinned. +- **ASCCONV doubles carry twelve significant figures.** That reproduces all 919 + distinct float literals in the reference archives, and so does Python's + `repr` -- but `repr` spells a freshly computed value with its binary tail + (`201.26200000000003` where the console writes `201.262`), so it is the wrong + choice for the one job the formatter has. - **Byte-exact round-trip is not the goal, because the console is not byte-stable either.** Re-saving an unmodified protocol regenerates all 67 GUIDs, rewrites `sCoilSelectMeas.aRxCoilSelectData[N].tCheckUUID` and the GUID @@ -370,6 +433,26 @@ readers be checked against each other. instances; reading there yields an empty tree that looks like a corrupt file. The real row's baseline is the compatibility gate the scanner checks: `MAJORVERSION:VA60A, PROTOCOL:66010002, ADDIN:NXMAINLINE, EDF:1, SEQUENCE:1`. +- **Two scanners differ only in the churn fields, plus the coils.** P1 and P2 + are the same protocol imported onto two XA60 systems. Five of eighteen + protocols are byte-identical; the other thirteen differ *only* in + `tCheckUUID`, `sWipMemBlock.tFree` and the date-and-time hiding in + `sSpecPara.lFinalMatrixSize*` -- every one already on the churn list above, + which was derived from re-saving one archive and is here confirmed on a + completely independent axis. No acquisition parameter differs. The single + real difference is hardware: `aRxCoilSelectData[1].aFFT_SCALE` has 58 + entries on P1 and 20 on P2, on the one scan using a second coil array. A + generator moving a protocol between scanners must not copy that across. +- **A readable archive can hold no protocols at all.** Exporting an empty + folder node rather than the protocol tree yields a valid SQLite file with + the directory scaffolding, a `Root` label and nothing else -- five + `Instance` rows against a real export's sixty-seven. It is an export + mistake, not a corrupt file, so `read` must not raise; but a corpus sweep + asserting things about scans has nothing to say about one and would report + the mistake as a reader failure. `conftest.EXAR_PROTOCOL_FILES` partitions + the corpus, and the sweeps that need scans take `protocol_archive_path` + while the structural ones (envelope, hashing, GUID layout) still take + `archive_path` and are exercised by it. - Everything so far is XA60 (`VA60A`). No XA30 archive has been seen, so the claim that the model is release-independent is untested -- that is the first thing to check when one arrives. diff --git a/examples/VE11C/31P CSI 20230503 NOE.pdf b/examples/VE11C/31P CSI 20230503 NOE.pdf new file mode 100755 index 0000000..3779f9f Binary files /dev/null and b/examples/VE11C/31P CSI 20230503 NOE.pdf differ diff --git a/examples/VE11C/BEEST_SPICE_11112025.pdf b/examples/VE11C/BEEST_SPICE_11112025.pdf new file mode 100755 index 0000000..ada15c0 Binary files /dev/null and b/examples/VE11C/BEEST_SPICE_11112025.pdf differ diff --git a/examples/XA60/31P CSI 20230503 NOE.pdf b/examples/XA60/31P CSI 20230503 NOE.pdf new file mode 100644 index 0000000..762a0d2 Binary files /dev/null and b/examples/XA60/31P CSI 20230503 NOE.pdf differ diff --git a/examples/XA60/CMRR_optionscan_P1.exar1 b/examples/XA60/CMRR_optionscan_P1.exar1 new file mode 100755 index 0000000..1786313 Binary files /dev/null and b/examples/XA60/CMRR_optionscan_P1.exar1 differ diff --git a/examples/XA60/CMRR_optionscan_P1.pdf b/examples/XA60/CMRR_optionscan_P1.pdf new file mode 100755 index 0000000..c02c2b3 Binary files /dev/null and b/examples/XA60/CMRR_optionscan_P1.pdf differ diff --git a/examples/XA60/MEMPRAGE_optionscan_P1.exar1 b/examples/XA60/MEMPRAGE_optionscan_P1.exar1 new file mode 100755 index 0000000..c639df1 Binary files /dev/null and b/examples/XA60/MEMPRAGE_optionscan_P1.exar1 differ diff --git a/examples/XA60/MEMPRAGE_optionscan_P1.pdf b/examples/XA60/MEMPRAGE_optionscan_P1.pdf new file mode 100755 index 0000000..058d350 Binary files /dev/null and b/examples/XA60/MEMPRAGE_optionscan_P1.pdf differ diff --git a/examples/XA60/NAV_optionscan_P1.exar1 b/examples/XA60/NAV_optionscan_P1.exar1 new file mode 100755 index 0000000..8fa6138 Binary files /dev/null and b/examples/XA60/NAV_optionscan_P1.exar1 differ diff --git a/examples/XA60/NAV_optionscan_P1.pdf b/examples/XA60/NAV_optionscan_P1.pdf new file mode 100755 index 0000000..d72ecd8 Binary files /dev/null and b/examples/XA60/NAV_optionscan_P1.pdf differ diff --git a/examples/XA60/Potpourri_P1.exar1 b/examples/XA60/Potpourri_P1.exar1 new file mode 100755 index 0000000..877006b Binary files /dev/null and b/examples/XA60/Potpourri_P1.exar1 differ diff --git a/examples/XA60/Potpourri_P1.pdf b/examples/XA60/Potpourri_P1.pdf new file mode 100644 index 0000000..5e0cb96 Binary files /dev/null and b/examples/XA60/Potpourri_P1.pdf differ diff --git a/examples/XA60/Potpourri_P1_changed.exar1 b/examples/XA60/Potpourri_P1_changed.exar1 new file mode 100755 index 0000000..0c83713 Binary files /dev/null and b/examples/XA60/Potpourri_P1_changed.exar1 differ diff --git a/examples/XA60/Potpourri_P1_changed.pdf b/examples/XA60/Potpourri_P1_changed.pdf new file mode 100644 index 0000000..6241f09 Binary files /dev/null and b/examples/XA60/Potpourri_P1_changed.pdf differ diff --git a/examples/XA60/Potpourri.exar1 b/examples/XA60/Potpourri_P2.exar1 similarity index 100% rename from examples/XA60/Potpourri.exar1 rename to examples/XA60/Potpourri_P2.exar1 diff --git a/examples/XA60/Potpourri.pdf b/examples/XA60/Potpourri_P2.pdf similarity index 100% rename from examples/XA60/Potpourri.pdf rename to examples/XA60/Potpourri_P2.pdf diff --git a/examples/XA60/Potpourri_changed.exar1 b/examples/XA60/Potpourri_P2_changed.exar1 similarity index 100% rename from examples/XA60/Potpourri_changed.exar1 rename to examples/XA60/Potpourri_P2_changed.exar1 diff --git a/pyproject.toml b/pyproject.toml index 65a3f99..8fb04e1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -88,4 +88,6 @@ skip = "./examples,./tests/golden" # case-sensitively, so the lowercase spellings need their own entries: the # exar preview paths write the echo time as "sub.0.msr.te.0", and "TE" alone # does not cover that -- codespell reads the bare "te" as the/be/we/to. -ignore-words-list = "TE,TR,te,tr,ADDIN" +# NOE is the Nuclear Overhauser Effect, which names one of the spectroscopy +# examples and so appears in the scan-count and sequence tests. +ignore-words-list = "TE,TR,te,tr,ADDIN,NOE" diff --git a/src/siemens_protocol/exar/archive.py b/src/siemens_protocol/exar/archive.py index 66f64d4..8b2a7cd 100644 --- a/src/siemens_protocol/exar/archive.py +++ b/src/siemens_protocol/exar/archive.py @@ -341,8 +341,15 @@ def label_of(self, instance: Instance) -> str: Names live on a separate ``EdfString`` node rather than inside the protocol, so that renaming a scan does not rewrite -- and so does not - re-hash -- the protocol itself. The string content is a locale table - whose empty-string key holds the default. + re-hash -- the protocol itself. + + The string content is a locale table, and the key is not always the + same. Most archives put the default under ``""``, but some write + ``"en"`` instead, with no empty key at all -- both spellings occur in + the shipped corpus. Reading only ``""`` yields a nameless tree on those, + which looks like a reader that cannot find the labels rather than one + looking under the wrong key. Any locale is better than no name, so the + empty key wins, then English, then whatever is there. Parameters ---------- @@ -360,7 +367,12 @@ def label_of(self, instance: Instance) -> str: holder = self.by_element.get(element) if holder is None: return "" - return self.document(holder).get("Texts", {}).get("", "") + texts = self.document(holder).get("Texts", {}) + locales = {k: v for k, v in texts.items() if k != "$id" and isinstance(v, str)} + for key in ("", "en"): + if locales.get(key): + return locales[key] + return next((v for _k, v in sorted(locales.items()) if v), "") @property def program(self) -> Instance | None: diff --git a/src/siemens_protocol/exar/patch.py b/src/siemens_protocol/exar/patch.py index eb87881..105bfb2 100644 --- a/src/siemens_protocol/exar/patch.py +++ b/src/siemens_protocol/exar/patch.py @@ -1,22 +1,39 @@ -"""Write a printed parameter back into a protocol, in both places it lives. - -A value the console displays is stored twice. ``Preview`` holds what the -console lists and what the PDF export prints -- ``TR``, in milliseconds, as a -float -- while the XProtocol text's ASCCONV block holds what the sequence -actually runs -- ``alTR[0]``, in microseconds, as an integer. Patching one and -not the other is silently wrong in opposite directions: edit only the preview -and the console lists a number the scan will not use; edit only the ASCCONV and -the listing goes stale. Every mapping here therefore names both. +"""Write a printed parameter back into a protocol, in every place it lives. + +A displayed value can be stored in more than one place, and the shapes differ: + +``Preview`` and ASCCONV together + ``TR`` is ``Preview["sub.0.msr.tr.0"]`` in milliseconds and ``alTR[0]`` in + microseconds. Patching one and not the other is silently wrong in opposite + directions -- the console lists a number the scan will not use, or the + listing goes stale. +An ASCCONV *array* + ``FOV Read`` and ``Slice Thickness`` are replicated across every element of + ``sSliceArray.asSlice[]`` -- three of them on a localizer, sixty-four on a + multi-slice EPI. Writing element zero alone leaves the rest at the old + value, which loads, lists correctly, and is wrong. +A value derived from another + ``FOV Phase`` is a percentage on the card but millimetres in the protocol: + ``dPhaseFOV`` is ``dReadoutFOV`` times that percentage. It cannot be + written without reading the read FOV first, which is what :attr:`Mapping.basis` + is for. ``Preview`` also rounds it -- 96.7 against a stored 96.6667 -- so + for this one parameter the two stores genuinely disagree slightly. +ASCCONV alone + Nothing on the Special card appears in ``Preview``; the console lists only + common parameters. Those mappings carry ``preview_path=None`` and there is + nothing to keep in sync. + +The Special card is also why mappings carry :attr:`Mapping.sequences`. +``sWipMemBlock`` is scratch memory the sequence binary interprets as it likes, +so an index has no global meaning: ``alFree[0]`` is MT Flip Angle on +``can_neuromelanin`` and a packed word of ten checkbox flags on CMRR's +multiband sequences. A table that treated it as one parameter would write a +flip angle into CMRR's flags. What this module deliberately does *not* do is recompute derived values. The console does: changing TR moved ``lScanTimeSec`` and ``lTotalScanTimeSec`` in -the reference pair. A patched archive carries the old scan time, and +the reference pairs. A patched archive carries the old scan time, and :class:`Manifest` says so rather than leaving it to be discovered later. - -Mappings are keyed by preview path, not by printed label, because labels are -not unique within a protocol -- ``Slices`` is both ``sub.0.msr.sg.0.size`` and -``sub.0.msr.total_size``. A label is accepted as a convenience and resolved -against the protocol, and an ambiguous one is refused rather than guessed. """ from __future__ import annotations @@ -35,90 +52,392 @@ @dataclass(frozen=True) class Mapping: - """One printed parameter, and the two places its value is stored. + """One printed parameter, and everywhere its value is stored. Attributes ---------- - preview_path : str - Key into the protocol's ``Preview`` map, for example ``sub.0.msr.tr.0``. + label : str + The label the console and the PDF print, for example ``TR``. ascconv_key : str - Assignment in the ASCCONV block, for example ``alTR[0]``. + Assignment in the ASCCONV block. May contain ``[*]``, which stands for + every index the block actually defines -- the slice arrays are sized + per protocol, so the set is read from the document rather than assumed. + evidence : str + How the mapping was established. These were derived from a corpus + rather than documentation, and a controlled edit is much stronger + evidence than mere agreement, so the difference is recorded. + preview_path : str or None + Key into the protocol's ``Preview`` map, or ``None`` when the console + does not list this parameter -- true of everything on the Special card. scale : float - Multiplier taking the preview value to the ASCCONV value. ``1000`` for - the times, which the preview holds in milliseconds and ASCCONV in + Multiplier taking the displayed value to the stored one. ``1000`` for + the times, which are displayed in milliseconds and stored in microseconds. - label : str - The label the console and the PDF print, for reference and for - resolving a caller's label. Not unique across a protocol. - evidence : str - How the mapping was established. Kept because these were derived from - a corpus rather than from documentation, and a later reader needs to - know which are backed by a controlled edit and which by agreement. + basis : str or None + Another ASCCONV key whose value also multiplies the written one, for a + parameter stored relative to a second field. ``[*]`` here resolves to + the same index as the target, which is what makes ``dPhaseFOV`` follow + its own slice's ``dReadoutFOV``. + sequences : tuple of str + Sequence names this mapping applies to, matched against the protocol's + ``seq_subpath``. Empty means every sequence. Non-empty is mandatory for + anything in ``sWipMemBlock``. + choices : tuple of tuple + ``(displayed text, stored integer)`` pairs for a parameter the card + shows as a word rather than a number. Established by toggling one + option per export and reading which integer moved. + bit : int or None + Position of this parameter's flag within ``ascconv_key``, for a + checkbox packed into a shared word. Writing one is a read-modify-write + of that word, and an absent word counts as zero. + when : tuple of str or None + An ``(ASCCONV key, literal)`` pair that must hold for this mapping to + apply, which is how one label can be stored two different ways. Slice + thickness is the case: on a 2D acquisition ``dThickness`` is the slice, + and on a 3D one it is the whole *slab*, so the two need separate + entries selected by ``sKSpace.ucDimension``. """ - preview_path: str - ascconv_key: str - scale: float label: str + ascconv_key: str evidence: str + preview_path: str | None = None + scale: float = 1.0 + basis: str | None = None + sequences: tuple[str, ...] = () + choices: tuple[tuple[str, int], ...] = () + bit: int | None = None + when: tuple[str, str] | None = None + + @property + def is_sequence_specific(self) -> bool: + """Return whether this mapping is restricted to named sequences. + + Returns + ------- + bool + ``True`` when :attr:`sequences` is non-empty. + """ + return bool(self.sequences) + +#: Preview key holding the sequence name a protocol runs. +SEQUENCE_PATH = "sub.0.msr.seq_subpath" -#: The mappings this module will write, keyed by preview path. +#: Every mapping this module will write. #: -#: Every entry was established against ``examples/XA60/`` rather than from any -#: Siemens document. Two kinds of evidence appear, and they are not equal. TR -#: is backed by a *controlled edit*: ``Potpourri_changed.exar1`` is the same -#: export re-saved with TR altered on five scans, and the diff moved exactly -#: the preview entry and the ASCCONV key named here. The rest are backed by -#: *agreement*: across every protocol in the corpus the preview value equals -#: the ASCCONV value under the stated scale, no other ASCCONV key agrees, and -#: the parameter takes enough distinct values that the agreement cannot be -#: coincidence. +#: All of it was established against ``examples/XA60/`` rather than from any +#: Siemens document, and the ``evidence`` field says how. A *controlled edit* +#: is the strong form: a pair of exports differing by one deliberate change, +#: which shows directly that a field moved with a label. *Agreement* is the +#: weak form: the two stores hold the same number under the stated scale +#: across every protocol, with no rival key and enough distinct values to make +#: coincidence implausible. #: -#: That second bar is what keeps this table short. ``FOV Read`` looks -#: mappable and is left out: ``sSliceArray.asSlice[0].dReadoutFOV`` and -#: ``...dPhaseFOV`` hold the same number in every example, because FOV Phase -#: is 100% throughout the corpus, so the data cannot say which one the label -#: belongs to. An export with a non-square FOV would settle it. Adding an -#: entry on the strength of its name alone is how a patcher comes to write a -#: plausible value into the wrong field. -MAPPINGS: dict[str, Mapping] = { - "sub.0.msr.tr.0": Mapping( +#: Nothing is added on the strength of its name. ``FOV Read`` sat out of this +#: table until an export arrived with FOV Phase off 100%, because until then +#: ``dReadoutFOV`` and ``dPhaseFOV`` held the same number in every protocol +#: and the data could not say which one the label meant. +MAPPINGS: tuple[Mapping, ...] = ( + Mapping( + label="TR", preview_path="sub.0.msr.tr.0", ascconv_key="alTR[0]", scale=1000.0, - label="TR", - evidence="controlled edit: Potpourri vs Potpourri_changed, 5 scans, 20 distinct values", + evidence="controlled edit: P2 pair, 5 scans; and P1 pair", ), - "sub.0.msr.te.0": Mapping( + Mapping( + label="TE", preview_path="sub.0.msr.te.0", ascconv_key="alTE[0]", scale=1000.0, - label="TE", - evidence="agreement across 36 protocols, 16 distinct values, no rival key", + evidence="controlled edit: P1 pair, 4 scans. Multi-echo prints TE 1..TE 4 " + "and Preview carries only the first; alTE[1..3] have no preview side.", ), - "sub.0.msr.angle_array.0": Mapping( + Mapping( + label="Flip Angle", preview_path="sub.0.msr.angle_array.0", ascconv_key="adFlipAngleDegree[0]", - scale=1.0, - label="Flip Angle", - evidence="agreement across 34 protocols, 9 distinct values, no rival key", + evidence="controlled edit: P1 pair, localizer", ), - "sub.0.msr.matrix": Mapping( + Mapping( + label="Base Resolution", preview_path="sub.0.msr.matrix", ascconv_key="sKSpace.lBaseResolution", - scale=1.0, - label="Base Resolution", - evidence="agreement across 36 protocols, 7 distinct values, no rival key", + evidence="controlled edit: P1 pair, 2 scans", ), - "sub.0.msr.ips": Mapping( + Mapping( + label="Slices per Slab", preview_path="sub.0.msr.ips", ascconv_key="sKSpace.lImagesPerSlab", - scale=1.0, - label="Slices per Slab", evidence="agreement across 14 protocols, 4 distinct values, no rival key", ), -} + Mapping( + label="FOV Read", + preview_path="sub.0.msr.readout_fov", + ascconv_key="sSliceArray.asSlice[*].dReadoutFOV", + evidence="controlled edit: P1 pair, CMRR 207->206 mm. Replicated across " + "every slice -- 3 on a localizer, 64 on the CMRR EPI.", + ), + Mapping( + label="Slice Thickness", + preview_path="sub.0.msr.sl_thick", + ascconv_key="sSliceArray.asSlice[*].dThickness", + when=("sKSpace.ucDimension", "2"), + evidence="controlled edit: P1 pair, localizer 7.0->7.5 and CMRR 2.3->2.2, " + "both 2D. Replicated per slice.", + ), + Mapping( + label="Slice Thickness", + preview_path="sub.0.msr.sl_thick", + ascconv_key="sSliceArray.asSlice[*].dThickness", + basis="sKSpace.lImagesPerSlab", + when=("sKSpace.ucDimension", "4"), + evidence="agreement: on all 8 three-dimensional protocols dThickness is the " + "whole slab -- exactly the displayed thickness times lImagesPerSlab. No " + "controlled edit has moved a slab thickness, so this is the weaker form; " + "the 2D entry above is what the edit covered.", + ), + Mapping( + label="FOV Phase", + preview_path="sub.0.msr.phase_fov", + ascconv_key="sSliceArray.asSlice[*].dPhaseFOV", + scale=0.01, + basis="sSliceArray.asSlice[*].dReadoutFOV", + evidence="controlled edit: P1 pair, 100%->96.7% and 100%->97.7%. Stored as " + "millimetres, not percent: dPhaseFOV = dReadoutFOV * percent / 100.", + ), + # ---- The Special card. ASCCONV only, and meaningful per sequence. ---- + Mapping( + label="MT Flip Angle", + ascconv_key="sWipMemBlock.alFree[0]", + sequences=("can_neuromelanin",), + evidence="controlled edit: P1 pair, 370->360 degrees", + ), + Mapping( + label="MT Offset", + ascconv_key="sWipMemBlock.alFree[1]", + sequences=("can_neuromelanin",), + evidence="controlled edit: P1 pair, 1500->1490 Hz", + ), + Mapping( + label="Add. grad time", + ascconv_key="sWipMemBlock.adFree[3]", + sequences=("tfl_mgh_epinav_ABCD",), + evidence="controlled edit: P1 pair, 0.00->0.10 ms", + ), + # ---- CMRR's packed flags word. One bit per Special-card checkbox, + # each pinned by an export toggling that box alone, and consistent + # across the BOLD, SE and diffusion sequences. + Mapping( + label="Single-band images", + ascconv_key="sWipMemBlock.alFree[0]", + bit=0, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 0", + ), + Mapping( + label="PF omits higher k-space", + ascconv_key="sWipMemBlock.alFree[0]", + bit=1, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 1", + ), + Mapping( + label="SENSE1 coil combine", + ascconv_key="sWipMemBlock.alFree[0]", + bit=4, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 4", + ), + Mapping( + label="Invert RO/PE polarity", + ascconv_key="sWipMemBlock.alFree[0]", + bit=8, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 8", + ), + Mapping( + label="MB RF phase scramble", + ascconv_key="sWipMemBlock.alFree[0]", + bit=9, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 9", + ), + Mapping( + label="Time-shifted MB RF", + ascconv_key="sWipMemBlock.alFree[0]", + bit=10, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 10", + ), + Mapping( + label="MB LeakBlock kernel", + ascconv_key="sWipMemBlock.alFree[0]", + bit=12, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 12", + ), + Mapping( + label="MB dual kernel", + ascconv_key="sWipMemBlock.alFree[0]", + bit=16, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 16", + ), + Mapping( + label="Disable freq. update", + ascconv_key="sWipMemBlock.alFree[0]", + bit=18, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 18", + ), + Mapping( + label="Force equal slice timing", + ascconv_key="sWipMemBlock.alFree[0]", + bit=20, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 20", + ), + Mapping( + label="Opt. MB RF pulse BW", + ascconv_key="sWipMemBlock.alFree[0]", + bit=22, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 22", + ), + Mapping( + label="Suppress 16-bit DICOM", + ascconv_key="sWipMemBlock.alFree[0]", + bit=25, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 25", + ), + Mapping( + label="Disable B1 control loop", + ascconv_key="sWipMemBlock.alFree[0]", + bit=27, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 27", + ), + Mapping( + label="Force GPA balance", + ascconv_key="sWipMemBlock.alFree[0]", + bit=28, + sequences=("cmrr_mbep2d_bold", "cmrr_mbep2d_se", "cmrr_mbep2d_diff"), + evidence="controlled edit: CMRR_optionscan_P1, single-option toggle -> bit 28", + ), + # ---- The ABCD navigated sequences. Shared between the MPRAGE and + # SPACE variants, which agree on every index below. + Mapping( + label="Feedback Delay", + ascconv_key="sWipMemBlock.alFree[6]", + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. ms, written directly.", + ), + Mapping( + label="Remeasure", + ascconv_key="sWipMemBlock.alFree[9]", + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. TRs, written directly.", + ), + Mapping( + label="Reacq. threshold", + ascconv_key="sWipMemBlock.adFree[2]", + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. written directly.", + ), + Mapping( + label="Moco ref. image", + ascconv_key="sWipMemBlock.alFree[7]", + choices=(("Use Temp Ref", 1), ("New Sess Ref", 2), ("Use Sess Ref", 3)), + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. three-way choice.", + ), + Mapping( + label="Apply moco to", + ascconv_key="sWipMemBlock.alFree[8]", + choices=(("neither", 1), ("nav only", 2), ("parent and nav", 3)), + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. three-way choice.", + ), + Mapping( + label="Apply freq to", + ascconv_key="sWipMemBlock.alFree[10]", + choices=(("neither", 1), ("parent and nav", 3)), + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. only two states seen; 2 unobserved.", + ), + Mapping( + label="K-space streaming", + ascconv_key="sWipMemBlock.alFree[14]", + choices=(("None", 1), ("File", 2), ("Network", 3)), + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. three-way choice.", + ), + Mapping( + label="ABCD navigator", + ascconv_key="sWipMemBlock.alFree[15]", + choices=(("Off", 1), ("On", 2)), + sequences=("tfl_mgh_epinav_ABCD", "space_mgh_epinav_ABCD"), + evidence="controlled edit: NAV_optionscan_P1, single-option toggle. two-way choice.", + ), + # alFree[12] carries a different parameter on each of the two, which is + # why the nav family cannot share one entry for it. + Mapping( + label="Nav. location", + ascconv_key="sWipMemBlock.alFree[12]", + choices=(("Before", 1), ("After", 2), ("None", 3)), + sequences=("tfl_mgh_epinav_ABCD",), + evidence="controlled edit: NAV_optionscan_P1. Setting None also clears Remeasure.", + ), + Mapping( + label="Include Nav.", + ascconv_key="sWipMemBlock.alFree[12]", + choices=(("Off", 1), ("On", 2)), + sequences=("space_mgh_epinav_ABCD",), + evidence="controlled edit: NAV_optionscan_P1. Same index as Nav. location on the " + "MPRAGE variant, and a different parameter -- the reason these are per sequence.", + ), + Mapping( + label="Readout polarity", + ascconv_key="sWipMemBlock.alFree[1]", + choices=(("Positive", 1), ("Negative", 2)), + sequences=("tfl_mgh_epinav_ABCD",), + evidence="controlled edit: NAV_optionscan_P1", + ), + Mapping( + label="Protocol filename", + ascconv_key="sWipMemBlock.alFree[1]", + choices=(("Generic", 1), ("MPRAGE", 2), ("T2-SPACE", 3)), + sequences=("ep_moco_nav_set_ABCD",), + evidence="controlled edit: NAV_optionscan_P1. alFree[1] again, and again a " + "different parameter -- Readout polarity on the MPRAGE sequence.", + ), + # ---- The multi-echo MEMPRAGE. ---- + Mapping( + label="Readout polarity", + ascconv_key="sWipMemBlock.alFree[1]", + choices=(("Positive", 1), ("Negative", 2)), + sequences=("tfl_mgh_multiecho",), + evidence="controlled edit: MEMPRAGE_optionscan_P1", + ), + Mapping( + label="Gradient spoiling", + ascconv_key="sWipMemBlock.alFree[5]", + choices=(("Siemens", 1), ("Integral", 2)), + sequences=("tfl_mgh_multiecho",), + evidence="controlled edit: MEMPRAGE_optionscan_P1. Echo Spacing follows as a " + "consequence and is not written here.", + ), + Mapping( + label="Averaging", + ascconv_key="sWipMemBlock.alFree[4]", + choices=(("None", 1), ("Linear", 2), ("RMS", 3), ("RMS only", 4), ("Mean", 5)), + sequences=("tfl_mgh_multiecho",), + evidence="controlled edit: MEMPRAGE_optionscan_P1, all five states observed", + ), +) @dataclass(frozen=True) @@ -197,12 +516,21 @@ class Manifest: that still hold whatever the source archive said. stale : list of str Values the console would have recomputed and this module did not. + approximate : list of str + Values written exactly as asked where the console would instead pick + the nearest value its hardware can realise. ``FOV Phase`` is the case: + the console quantises it to an achievable ratio -- 29/30 of the read + FOV where 96.7% was displayed -- and the card prints that rounded to a + tenth of a percent, so a percentage cannot reconstruct the millimetres + it came from. The value written is the one requested, and differs from + the console's by less than the rounding of the printed figure. """ applied: list[Applied] = field(default_factory=list) skipped: list[Skipped] = field(default_factory=list) inherited: int = 0 stale: list[str] = field(default_factory=list) + approximate: list[str] = field(default_factory=list) @property def complete(self) -> bool: @@ -233,6 +561,11 @@ def report(self) -> str: for miss in self.skipped: lines.append(f"skip {miss.step}: {miss.label}={miss.value} -- {miss.reason}") lines.append(f"inherited {self.inherited} preview value(s) from the source archive") + if self.approximate: + lines.append( + "written as asked, but the console quantises these: " + + ", ".join(sorted(set(self.approximate))) + ) if self.stale: lines.append("not recomputed, the console would have: " + ", ".join(self.stale)) return "\n".join(lines) @@ -314,6 +647,92 @@ def write_ascconv(text: str, key: str, literal: str) -> str: return text[: found.start("value")] + literal + text[found.end("value") :] +def omits_zero(key: str) -> bool: + """Return whether an assignment is left out entirely when it holds zero. + + ``sWipMemBlock`` is written sparsely: its arrays list only the indices that + carry a value, in ascending order, and the console adds and removes lines + as options are set and cleared. A CMRR protocol with every Special-card box + unticked has no ``alFree[0]`` at all, and setting ``Remeasure`` to zero + deleted its line rather than writing ``0``. Both were observed directly in + the option-scan exports. + + Parameters + ---------- + key : str + A concrete ASCCONV key. + + Returns + ------- + bool + ``True`` for a sparse array element. + """ + return bool(re.match(r"sWipMemBlock\.(al|ad)Free\[\d+\]$", key)) + + +def remove_ascconv(text: str, key: str) -> str: + """Delete one ASCCONV assignment, line and all. + + Parameters + ---------- + text : str + The XProtocol text. + key : str + The assignment to remove. + + Returns + ------- + str + The text without that line, unchanged when it was already absent. + """ + start, end = ascconv_bounds(text) + if start < 0: + return text + line = re.compile(rf"^[ \t]*{re.escape(key)}[ \t]*=.*?\r?\n", re.M) + found = line.search(text, start, end) + return text[: found.start()] + text[found.end() :] if found else text + + +def insert_ascconv(text: str, key: str, literal: str) -> str: + """Add an assignment that the document does not yet carry. + + Sparse arrays are written in ascending index order, so a new element goes + among its siblings rather than at the end of the block: the console emits + ``alFree[1]``, ``alFree[4]``, ``alFree[6]`` and so on, and appending would + break that order. + + Parameters + ---------- + text : str + The XProtocol text. + key : str + The assignment to add, for example ``sWipMemBlock.alFree[0]``. + literal : str + The value to write. + + Returns + ------- + str + The text with the assignment inserted, unchanged when there is no + sibling to place it beside. + """ + start, end = ascconv_bounds(text) + match = re.fullmatch(r"(.*)\[(\d+)\]", key) + if start < 0 or match is None: + return text + stem, index = match.group(1), int(match.group(2)) + sibling = re.compile(rf"^([ \t]*){re.escape(stem)}\[(\d+)\]([ \t]*=[ \t]*).*?\r?\n", re.M) + found = [m for m in sibling.finditer(text, start, end)] + if not found: + return text + after = next((m for m in found if int(m.group(2)) > index), None) + at = after.start() if after is not None else found[-1].end() + model = after if after is not None else found[-1] + ending = "\r\n" if model.group(0).endswith("\r\n") else "\n" + line = f"{model.group(1)}{key}{model.group(3)}{literal}{ending}" + return text[:at] + line + text[at:] + + def _assignment(key: str) -> re.Pattern[str]: """Build the pattern matching one ASCCONV assignment. @@ -338,6 +757,13 @@ def format_like(value: float, existing: str) -> str: interchangeable to every reader of the file, so the existing literal decides which is written back. + Doubles are written to twelve significant figures, which is what the + console writes and what reproduces all 919 distinct float literals in the + reference archives. Python's ``repr`` reproduces them too, but it spells a + freshly computed value with its full binary tail -- ``201.26200000000003`` + where the console would write ``201.262`` -- so it is the wrong choice for + the one job this function exists to do. + Parameters ---------- value : float @@ -352,39 +778,212 @@ def format_like(value: float, existing: str) -> str: """ if re.fullmatch(r"[-+]?\d+", existing.strip()): return str(int(round(value))) - return repr(float(value)) + written = f"{float(value):.12g}" + return written if ("." in written or "e" in written or "E" in written) else written + ".0" + + +def sequence_of(protocol: Protocol) -> str: + """Return the sequence a protocol runs, as ``seq_subpath`` spells it. + + Parameters + ---------- + protocol : Protocol + The protocol to inspect. + + Returns + ------- + str + For example ``cmrr_mbep2d_bold``, or an empty string when the preview + does not carry one. + """ + entry = protocol.preview.get(SEQUENCE_PATH) + return str(entry.value) if entry is not None and entry.value is not None else "" -def resolve(protocol: Protocol, name: str) -> tuple[str | None, str]: - """Turn a caller's label or preview path into a mapped preview path. +def applies_to(mapping: Mapping, protocol: Protocol) -> bool: + """Return whether a mapping is meaningful for this protocol. Parameters ---------- + mapping : Mapping + The mapping to test. protocol : Protocol - The protocol the name is being resolved against. + The protocol it would be written into. + + Returns + ------- + bool + ``True`` for an unrestricted mapping, or one naming this sequence. + """ + if mapping.sequences and sequence_of(protocol) not in mapping.sequences: + return False + if mapping.when is not None: + key, expected = mapping.when + return read_ascconv(protocol.xprotocol, key) == expected + return True + + +def expand(pattern: str, text: str) -> list[tuple[str, int | None]]: + """Resolve an ``[*]`` target against the indices a document defines. + + The slice arrays are sized per protocol -- three elements on a localizer, + sixty-four on a multi-slice EPI -- so the indices are read from the + document rather than assumed. A pattern that matches nothing yields an + empty list, which the caller reports rather than silently skipping. + + Parameters + ---------- + pattern : str + An ASCCONV key, possibly containing ``[*]``. + text : str + The XProtocol text to search. + + Returns + ------- + list of tuple + ``(concrete key, index)`` pairs in index order. The index is ``None`` + for a pattern with no ``[*]``. + """ + if "[*]" not in pattern: + return [(pattern, None)] + start, end = ascconv_bounds(text) + if start < 0: + return [] + prefix, suffix = pattern.split("[*]", 1) + found = re.compile(rf"^[ \t]*{re.escape(prefix)}\[(\d+)\]{re.escape(suffix)}[ \t]*=", re.M) + indices = sorted({int(m.group(1)) for m in found.finditer(text, start, end)}) + return [(f"{prefix}[{i}]{suffix}", i) for i in indices] + + +def resolve(protocol: Protocol, name: str) -> tuple[Mapping | None, str]: + """Turn a caller's label into the mapping that writes it. + + Parameters + ---------- + protocol : Protocol + The protocol the name is being resolved against, which decides which + sequence-specific mappings are in scope. name : str - A preview path, or a printed label such as ``TR``. + A printed label such as ``TR``, or a preview path. Returns ------- tuple - The resolved preview path and an empty reason, or ``None`` and the - reason it could not be resolved. + The mapping and an empty reason, or ``None`` and the reason it could + not be resolved. """ - if name in MAPPINGS: - return (name, "") wanted = name.strip().casefold() - hits = [m.preview_path for m in MAPPINGS.values() if m.label.strip().casefold() == wanted] + in_scope = [m for m in MAPPINGS if applies_to(m, protocol)] + hits = [m for m in in_scope if m.label.strip().casefold() == wanted] + if not hits: + hits = [m for m in in_scope if m.preview_path == name] if len(hits) == 1: return (hits[0], "") if len(hits) > 1: - return (None, f"label {name!r} maps to several parameters: {', '.join(sorted(hits))}") + keys = ", ".join(sorted(m.ascconv_key for m in hits)) + return (None, f"label {name!r} maps to several parameters: {keys}") + elsewhere = [m for m in MAPPINGS if m.label.strip().casefold() == wanted] + if elsewhere: + runs = sequence_of(protocol) or "an unnamed sequence" + wants = ", ".join(sorted({q for m in elsewhere for q in m.sequences})) + return (None, f"{name!r} is mapped for {wants}, but this protocol runs {runs}") printed = {e.label.strip().casefold() for e in protocol.preview.values()} if wanted in printed: return (None, f"{name!r} is printed by this protocol but no verified mapping writes it") return (None, f"no verified mapping for {name!r}") +def encode(mapping: Mapping, value: Any) -> tuple[float | None, str]: + """Turn a caller's value into the number to store. + + Parameters + ---------- + mapping : Mapping + The parameter being written. + value : Any + What the caller asked for: a number, or the text the card displays, + or a boolean for a flag. + + Returns + ------- + tuple + The numeric value and an empty reason, or ``None`` and the reason it + could not be encoded. + """ + if mapping.bit is not None: + truth = _as_bool(value) + if truth is None: + return (None, f"{mapping.label} is a checkbox; expected on/off, got {value!r}") + return (float(truth), "") + if mapping.choices: + table = {text.strip().casefold(): number for text, number in mapping.choices} + if isinstance(value, str): + found = table.get(value.strip().casefold()) + if found is None: + offered = ", ".join(text for text, _ in mapping.choices) + return (None, f"{value!r} is not a {mapping.label}; expected one of: {offered}") + return (float(found), "") + if value in {number for _text, number in mapping.choices}: + return (float(value), "") + offered = ", ".join(text for text, _ in mapping.choices) + return (None, f"{value!r} is not a {mapping.label}; expected one of: {offered}") + try: + return (float(value), "") + except (TypeError, ValueError): + return (None, f"{mapping.label} expects a number, got {value!r}") + + +def _as_bool(value: Any) -> bool | None: + """Read a checkbox value written as a bool, a number or the printed word. + + Parameters + ---------- + value : Any + The caller's value. + + Returns + ------- + bool or None + The interpreted state, or ``None`` when it is not a checkbox value. + """ + if isinstance(value, bool): + return value + if isinstance(value, (int, float)): + return bool(value) + if isinstance(value, str): + text = value.strip().casefold() + if text in {"on", "true", "yes", "1"}: + return True + if text in {"off", "false", "no", "0"}: + return False + return None + + +def set_bit(word: str | None, bit: int, on: bool) -> str: + """Set or clear one flag in a packed word. + + An absent assignment counts as zero: the console omits a flags word that + holds no bits, so a protocol with every checkbox clear simply has no + ``alFree[0]`` line at all. + + Parameters + ---------- + word : str or None + The current literal, or ``None`` when the assignment is absent. + bit : int + Bit position to write. + on : bool + The new state. + + Returns + ------- + str + The resulting literal. + """ + current = int(word) if word not in (None, "") else 0 + return str(current | (1 << bit) if on else current & ~(1 << bit)) + + def patch_document( protocol: Protocol, requests: MappingType[str, Any], step: str = "" ) -> tuple[dict[str, Any], list[Applied], list[Skipped]]: @@ -399,7 +998,7 @@ def patch_document( protocol : Protocol The protocol to patch. requests : mapping - Preview path or printed label to new preview-side value. + Printed label or preview path to new displayed value. step : str, optional Name of the step holding this protocol, used only for the records. @@ -416,11 +1015,11 @@ def patch_document( applied: list[Applied] = [] skipped: list[Skipped] = [] for name, value in requests.items(): - path, reason = resolve(protocol, name) - if path is None: + found, reason = resolve(protocol, name) + if found is None: skipped.append(Skipped(step=step, label=name, value=value, reason=reason)) continue - record, text = _apply_one(MAPPINGS[path], preview, text, value, step) + record, text = _apply_one(found, preview, text, value, step) (applied if isinstance(record, Applied) else skipped).append(record) document["Preview"] = preview document["Data"] = text @@ -434,18 +1033,19 @@ def _apply_one( value: Any, step: str, ) -> tuple[Applied | Skipped, str]: - """Write one mapped value into the preview map and the ASCCONV text. + """Write one mapped value into every location it occupies. Parameters ---------- mapping : Mapping The parameter being written. preview : dict - The protocol's preview map, mutated in place. + The protocol's preview map, mutated in place when the mapping has a + preview side. text : str The XProtocol text. value : Any - The new preview-side value. + The new displayed value. step : str Step name, for the record. @@ -454,46 +1054,143 @@ def _apply_one( tuple The record describing what happened, and the resulting text. """ - entry = preview.get(mapping.preview_path) - if not isinstance(entry, dict): - return ( - Skipped( - step=step, - label=mapping.label, - value=value, - reason=f"this protocol has no {mapping.preview_path} to write", - ), - text, - ) - existing = read_ascconv(text, mapping.ascconv_key) - if existing is None: - return ( - Skipped( - step=step, - label=mapping.label, - value=value, - reason=f"ASCCONV block has no {mapping.ascconv_key}", - ), - text, - ) - literal = format_like(float(value) * mapping.scale, existing) - previous = entry.get("Value") - entry["Value"] = type(previous)(value) if isinstance(previous, (int, float)) else value + + def refused(why: str) -> tuple[Skipped, str]: + return (Skipped(step=step, label=mapping.label, value=value, reason=why), text) + + targets = expand(mapping.ascconv_key, text) + if not targets: + return refused(f"ASCCONV block has no {mapping.ascconv_key}") + + entry = None + if mapping.preview_path is not None: + entry = preview.get(mapping.preview_path) + if not isinstance(entry, dict): + return refused(f"this protocol has no {mapping.preview_path} to write") + + number, why = encode(mapping, value) + if number is None: + return refused(why) + + first_before = first_after = "" + for key, index in targets: + existing = read_ascconv(text, key) + sparse = omits_zero(key) + if mapping.bit is not None: + # A flags word the console leaves out while every box is unticked + # is a legitimate state, not a missing target. + literal = set_bit(existing, mapping.bit, bool(number)) + if not first_before: + first_before, first_after = existing or "0", literal + text = _store(text, key, literal, existing, sparse) + continue + if existing is None and not sparse: + return refused(f"ASCCONV block has no {key}") + written = number * mapping.scale + if mapping.basis is not None: + basis_key = mapping.basis.replace("[*]", f"[{index}]") + basis = read_ascconv(text, basis_key) + if basis is None: + return refused(f"ASCCONV block has no {basis_key} to scale against") + written *= float(basis) + literal = format_like(written, existing if existing is not None else _model(key)) + if not first_before: + first_before, first_after = existing or "(absent)", literal + text = _store(text, key, literal, existing, sparse) + + previous = None + if entry is not None: + previous = entry.get("Value") + entry["Value"] = type(previous)(value) if isinstance(previous, (int, float)) else value + shown = entry["Value"] + else: + shown = value return ( Applied( step=step, label=mapping.label, - preview_path=mapping.preview_path, - ascconv_key=mapping.ascconv_key, + preview_path=mapping.preview_path or "(not listed by the console)", + ascconv_key=mapping.ascconv_key + (f" x{len(targets)}" if len(targets) > 1 else ""), previous=previous, - value=entry["Value"], - ascconv_previous=existing, - ascconv_value=literal, + value=shown, + ascconv_previous=first_before, + ascconv_value=first_after, ), - write_ascconv(text, mapping.ascconv_key, literal), + text, ) +def _model(key: str) -> str: + """Return a stand-in literal deciding how a *new* assignment is formatted. + + An element being created has no existing literal to copy the integer or + float spelling from, so the array it belongs to decides: ``alFree`` holds + integers and ``adFree`` doubles. + + Parameters + ---------- + key : str + The concrete ASCCONV key. + + Returns + ------- + str + ``"0"`` for an integer array, ``"0.0"`` otherwise. + """ + return "0" if ".alFree[" in key else "0.0" + + +def _store(text: str, key: str, literal: str, existing: str | None, sparse: bool) -> str: + """Write, create or delete one assignment as its array's rules require. + + A sparse array lists only the indices carrying a value, so writing zero + into one means removing its line, and writing a value into an absent one + means inserting it in index order. + + Parameters + ---------- + text : str + The XProtocol text. + key : str + The concrete ASCCONV key. + literal : str + The value to store. + existing : str or None + The literal currently in place, if any. + sparse : bool + Whether the assignment is omitted when it holds zero. + + Returns + ------- + str + The resulting text. + """ + if sparse and _is_zero(literal): + return remove_ascconv(text, key) if existing is not None else text + if existing is None: + return insert_ascconv(text, key, literal) + return write_ascconv(text, key, literal) + + +def _is_zero(literal: str) -> bool: + """Return whether a literal represents zero. + + Parameters + ---------- + literal : str + The literal to test. + + Returns + ------- + bool + ``True`` when it parses as zero. + """ + try: + return float(literal) == 0.0 + except ValueError: + return False + + def apply(archive: Archive, changes: MappingType[str, MappingType[str, Any]]) -> Manifest: """Apply per-step parameter changes to an archive, in memory. @@ -532,4 +1229,6 @@ def apply(archive: Archive, changes: MappingType[str, MappingType[str, Any]]) -> archive.replace_content(protocol.instance, document) if manifest.applied: manifest.stale = ["lScanTimeSec", "lTotalScanTimeSec"] + quantised = {m.label for m in MAPPINGS if m.basis is not None} + manifest.approximate = [a.label for a in manifest.applied if a.label in quantised] return manifest diff --git a/tests/conftest.py b/tests/conftest.py index 6b36e40..bee2473 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -180,6 +180,74 @@ def archive_path(request: pytest.FixtureRequest) -> str: return str(request.param) +def find_pdf(name: str) -> str: + """Locate one example PDF by file name, skipping the test if absent. + + Parameters + ---------- + name : str + Base file name, such as ``"CMRR_optionscan_P1.pdf"``. + + Returns + ------- + str + Full path to the PDF. + """ + for path, _version in EXAMPLE_FILES: + if os.path.basename(path) == name: + return path + pytest.skip(f"{name} is not among the available examples") + + +def exar_files_with_protocols() -> list[tuple[str, str | None]]: + """The archives that actually carry a protocol tree. + + An ``.exar1`` file can be a valid, readable archive and still hold no + protocols: exporting an empty folder node rather than the protocol tree + yields a database with the directory scaffolding and nothing else. That is + a real export mistake, not a corrupt file, so the reader must handle it -- + but a test that sweeps the corpus asserting things about scans has nothing + to say about one, and would report the mistake as a failure of the reader. + + Returns + ------- + list of tuple + ``(archive path, version or None)`` for archives holding at least one + protocol. + """ + from siemens_protocol.exar import read + + keep: list[tuple[str, str | None]] = [] + for path, version in EXAR_FILES: + try: + if read(path).program is not None: + keep.append((path, version)) + except Exception: # noqa: BLE001 - an unreadable archive is not this list's concern + continue + return keep + + +EXAR_PROTOCOL_FILES = exar_files_with_protocols() +EXAR_PROTOCOL_IDS = [os.path.basename(p) for p, _ in EXAR_PROTOCOL_FILES] + + +@pytest.fixture(params=[p for p, _ in EXAR_PROTOCOL_FILES], ids=EXAR_PROTOCOL_IDS) +def protocol_archive_path(request: pytest.FixtureRequest) -> str: + """Parametrize over the archives that carry a protocol tree. + + Parameters + ---------- + request : pytest.FixtureRequest + The parametrization hook. + + Returns + ------- + str + Path to one archive holding protocols. + """ + return str(request.param) + + def find_exar(name: str) -> str: """Locate one ``.exar1`` archive by file name, skipping the test if absent. diff --git a/tests/golden/VE11C-31P CSI 20230503 NOE.json b/tests/golden/VE11C-31P CSI 20230503 NOE.json new file mode 100644 index 0000000..a719a39 --- /dev/null +++ b/tests/golden/VE11C-31P CSI 20230503 NOE.json @@ -0,0 +1,2607 @@ +{ + "source_file": "examples/VE11C/31P CSI 20230503 NOE.pdf", + "software_version": "VE11C", + "detection": { + "method": "header-string", + "confidence": "high" + }, + "scanner": "SIEMENS MAGNETOM Prisma", + "page_count": 27, + "front_matter_pages": [ + 1 + ], + "scans": [ + { + "index": 0, + "name": "localizer", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\localizer", + "header": { + "ta": "0:19", + "pm": "REF", + "voxel_size_mm": "0.5×0.5×10.0", + "pat": "Off", + "rel_snr": "1.00", + "sequence": "fl" + }, + "provenance": { + "verdict": "stock", + "vendor": "Siemens", + "family": "FLASH -- spoiled gradient echo", + "evidence": [ + "sequence binary 'fl' is a Siemens kernel", + "no sequence-specific parameters printed" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "On", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "On", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slice group": "1", + "Slices": "5", + "Dist. factor": "20 %", + "Position": "Isocenter", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "Slice group #2": "2", + "Slices #2": "1", + "Dist. factor #2": "20 %", + "Position #2": "Isocenter", + "Orientation #2": "Transversal", + "Phase enc. dir. #2": "A >> P", + "Slice group #3": "3", + "Slices #3": "1", + "Dist. factor #3": "20 %", + "Position #3": "Isocenter", + "Orientation #3": "Coronal", + "Phase enc. dir. #3": "R >> L", + "AutoAlign": "---", + "Phase oversampling": "0 %", + "FoV read": "280 mm", + "FoV phase": "100.0 %", + "Slice thickness": "10.0 mm", + "TR": "20.0 ms", + "TE": "5.00 ms", + "Averages": "1", + "Concatenations": "7", + "Filter": "Normalize, Elliptical filter", + "Coil elements": "1H" + }, + "Contrast - Common": { + "TR": "20.0 ms", + "TE": "5.00 ms", + "TD": "0 ms", + "MTC": "Off", + "Magn. preparation": "None", + "Flip angle": "40 deg", + "Fat suppr.": "None", + "Water suppr.": "None", + "SWI": "Off" + }, + "Contrast - Dynamic": { + "Averages": "1", + "Averaging mode": "Short term", + "Reconstruction": "Magnitude", + "Measurements": "1", + "Multiple series": "Each measurement" + }, + "Resolution - Common": { + "FoV read": "280 mm", + "FoV phase": "100.0 %", + "Slice thickness": "10.0 mm", + "Base resolution": "256", + "Phase resolution": "50 %", + "Phase partial Fourier": "Off", + "Interpolation": "On" + }, + "Resolution - iPAT": { + "PAT mode": "None" + }, + "Resolution - Filter Image": { + "Image Filter": "Off", + "Distortion Corr.": "Off", + "Prescan Normalize": "Off", + "Normalize": "On", + "Unfiltered images": "Off", + "B1 filter": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "On" + }, + "Geometry - Common": { + "Slice group": "1", + "Slices": "5", + "Dist. factor": "20 %", + "Position": "Isocenter", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "Slice group #2": "2", + "Slices #2": "1", + "Dist. factor #2": "20 %", + "Position #2": "Isocenter", + "Orientation #2": "Transversal", + "Phase enc. dir. #2": "A >> P", + "Slice group #3": "3", + "Slices #3": "1", + "Dist. factor #3": "20 %", + "Position #3": "Isocenter", + "Orientation #3": "Coronal", + "Phase enc. dir. #3": "R >> L", + "FoV read": "280 mm", + "FoV phase": "100.0 %", + "Slice thickness": "10.0 mm", + "TR": "20.0 ms", + "Multi-slice mode": "Sequential", + "Series": "Interleaved", + "Concatenations": "7" + }, + "Geometry - AutoAlign": { + "Slice group": "1", + "Position": "Isocenter", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "Slice group #2": "2", + "Position #2": "Isocenter", + "Orientation #2": "Transversal", + "Phase enc. dir. #2": "A >> P", + "Slice group #3": "3", + "Position #3": "Isocenter", + "Orientation #3": "Coronal", + "Phase enc. dir. #3": "R >> L", + "AutoAlign": "---", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Rotation": "0.00 deg", + "Initial Orientation": "Sagittal" + }, + "Geometry - Saturation": { + "Saturation mode": "Standard", + "Fat suppr.": "None", + "Water suppr.": "None", + "Special sat.": "None" + }, + "System - Miscellaneous": { + "Positioning mode": "REF", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "L >> R", + "Coronal": "P >> A", + "Transversal": "F >> H", + "Coil Combine Mode": "Adaptive Combine", + "Save uncombined": "Off", + "Matrix Optimization": "Off", + "AutoAlign": "---", + "Coil Select Mode": "Off - All" + }, + "System - Adjustments": { + "B0 Shim mode": "Tune up", + "B1 Shim mode": "TrueForm", + "Adjust with body coil": "true", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "263 mm", + "R >> L": "350 mm", + "F >> H": "350 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm", + "Excitation": "Slice-sel." + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249501 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. Scale Cor.": "1.000", + "Reset": "Off", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "20.0 ms", + "Concatenations": "7", + "Segments": "1" + }, + "Physio - Cardiac": { + "Magn. preparation": "None", + "Fat suppr.": "None", + "Dark blood": "Off", + "FoV read": "280 mm", + "FoV phase": "100.0 %", + "Phase resolution": "50 %" + }, + "Physio - PACE": { + "Resp. control": "Off", + "Concatenations": "7" + }, + "Inline - Common": { + "Subtract": "Off", + "Measurements": "1", + "StdDev": "Off", + "Liver registration": "Off", + "Save original images": "On" + }, + "Inline - MIP": { + "MIP-Sag": "Off", + "MIP-Cor": "Off", + "MIP-Tra": "Off", + "MIP-Time": "Off", + "Save original images": "On" + }, + "Inline - Soft Tissue": { + "Wash - In": "Off", + "Wash - Out": "Off", + "TTP": "Off", + "PEI": "Off", + "MIP - time": "Off", + "Measurements": "1" + }, + "Inline - Composing": { + "Distortion Corr.": "Off" + }, + "Sequence - Part 1": { + "Introduction": "On", + "Dimension": "2D", + "Phase stabilisation": "Off", + "Asymmetric echo": "Off", + "Contrasts": "1", + "Flow comp.": "No", + "Multi-slice mode": "Sequential", + "Bandwidth": "180 Hz/Px" + }, + "Sequence - Part 2": { + "Segments": "1", + "Acoustic noise reduction": "None", + "RF pulse type": "Fast", + "Gradient mode": "Normal", + "Excitation": "Slice-sel.", + "RF spoiling": "On" + }, + "Sequence - Assistant": { + "Mode": "Off", + "Allowed delay": "0 s" + } + }, + "pages": [ + 2, + 3 + ] + }, + { + "index": 1, + "name": "AAHead_Scout", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\AAHead_Scout", + "header": { + "ta": "0:14", + "pm": "REF", + "voxel_size_mm": "1.6×1.6×1.6", + "pat": "3", + "rel_snr": "1.00", + "sequence": "fl" + }, + "provenance": { + "verdict": "stock", + "vendor": "Siemens", + "family": "FLASH -- spoiled gradient echo", + "evidence": [ + "sequence binary 'fl' is a Siemens kernel", + "no sequence-specific parameters printed" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "On", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "On", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slab group": "1", + "Slabs": "1", + "Dist. factor": "20 %", + "Position": "L0.0 A10.0 H0.0 mm", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "Phase oversampling": "0 %", + "Slice oversampling": "0.0 %", + "Slices per slab": "128", + "FoV read": "260 mm", + "FoV phase": "100.0 %", + "Slice thickness": "1.6 mm", + "TR": "3.15 ms", + "TE": "1.37 ms", + "Averages": "1", + "Concatenations": "1", + "Filter": "Prescan Normalize", + "Coil elements": "HE1-4" + }, + "Contrast - Common": { + "TR": "3.15 ms", + "TE": "1.37 ms", + "Flip angle": "8 deg" + }, + "Contrast - Dynamic": { + "Averages": "1", + "Averaging mode": "Short term", + "Reconstruction": "Magnitude", + "Measurements": "1" + }, + "Resolution - Common": { + "FoV read": "260 mm", + "FoV phase": "100.0 %", + "Slice thickness": "1.6 mm", + "Base resolution": "160", + "Phase resolution": "100 %", + "Slice resolution": "69 %", + "Phase partial Fourier": "6/8", + "Slice partial Fourier": "6/8", + "Trajectory": "Cartesian" + }, + "Resolution - iPAT": { + "PAT mode": "GRAPPA", + "Accel. factor PE": "3", + "Ref. lines PE": "24", + "Accel. factor 3D": "1", + "Reference scan mode": "Integrated" + }, + "Resolution - Filter Image": { + "Image Filter": "Off", + "Distortion Corr.": "Off", + "Prescan Normalize": "On", + "Unfiltered images": "Off", + "Normalize": "Off", + "B1 filter": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "Off" + }, + "Geometry - Common": { + "Slab group": "1", + "Slabs": "1", + "Dist. factor": "20 %", + "Position": "L0.0 A10.0 H0.0 mm", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "Slice oversampling": "0.0 %", + "Slices per slab": "128", + "FoV read": "260 mm", + "FoV phase": "100.0 %", + "Slice thickness": "1.6 mm", + "TR": "3.15 ms", + "Multi-slice mode": "Sequential", + "Series": "Ascending", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slab group": "1", + "Position": "L0.0 A10.0 H0.0 mm", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Rotation": "0.00 deg", + "Initial Orientation": "Transversal" + }, + "System - Miscellaneous": { + "Positioning mode": "REF", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combine Mode": "Adaptive Combine", + "Save uncombined": "Off", + "Matrix Optimization": "Off", + "Coil Select Mode": "Off - AutoCoilSelect" + }, + "System - Adjustments": { + "B0 Shim mode": "Tune up", + "B1 Shim mode": "TrueForm", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "263 mm", + "R >> L": "350 mm", + "F >> H": "350 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm", + "Excitation": "Non-sel." + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249501 MHz", + "Correction factor": "1", + "Gain": "Low", + "Img. Scale Cor.": "1.000", + "Reset": "Off", + "? 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Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "2800 ms" + }, + "Sequence - Common": { + "Delta frequency": "0.0 ppm", + "Phase cycling": "None", + "Bandwidth": "100000 Hz", + "Acquisition duration": "2 ms" + }, + "Sequence - Special": { + "Type of fit": "Linear 6-proj", + "VoI fit factor": "100 %", + "Force spherical fit VoI": "Off Force spherical fit VoI", + "Save plots to database": "Off", + "Refocus pulses": "Normal", + "Excite pulse duration": "6400 us", + "Refocus pulse duration": "6400 us", + "Bar FoV": "384 mm", + "Bar thickness": "10.0 mm", + "Inversion pulse": "Off", + "Multi-echo acquisition": "Off" + } + }, + "pages": [ + 14, + 15 + ] + }, + { + "index": 7, + "name": "SPECIAL_ACC", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\SPECIAL_ACC", + "header": { + "ta": "1:48", + "pm": "FIX", + "voi_mm": "32 ×20 ×34", + "rel_snr": "1.00", + "sequence": "svs_se" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'svs_se' is a Siemens kernel", + "prints 9 sequence-specific parameter(s) no signature accounts for, including Additional water suppression, Adiabatic Inversion, Excitation Pulse Duration" + ], + "special_parameters": 9 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Position": "L2.3 A45.1 H61.3 mm", + "Orientation": "C > T-24.6 > S4.6", + "Rotation": "1.262618 deg", + "VoI F >> H": "20 mm", + "VoI F >> H #2": "20 mm", + "VoI A >> P": "34 mm", + "TR": "3000 ms", + "TE": "12.00 ms", + "Averages": "32", + "Filter": "None", + "Coil elements": "HC3-6" + }, + "Contrast": { + "TR": "3000 ms", + "TE": "12.00 ms", + "Averages": "32", + "Flip angle": "90 deg", + "Water suppr.": "Water sat.", + "Water suppr. BW": "45 Hz", + "Spectral suppr.": "None", + "Measurements": "1" + }, + "Resolution - Common": { + "Prescan Normalize": "Off", + "Vector size": "2048" + }, + "Geometry - Common": { + "Position": "L2.3 A45.1 H61.3 mm", + "Orientation": "C > T-24.6 > S4.6", + "Rotation": "1.262618 deg", + "VoI F >> H": "20 mm", + "VoI R >> L": "32 mm", + "VoI A >> P": "34 mm" + }, + "Geometry - AutoAlign": { + "AutoAlign": "---", + "Initial Position": "L2.3 A45.1 H61.3", + "L": "2.3 mm", + "A": "45.1 mm", + "H": "61.3 mm", + "Initial Rotation": "91.26 deg", + "Initial Orientation": "C > T", + "C > T": "-24.6", + "> S": "4.6" + }, + "Geometry - Navigator": {}, + "System - Miscellaneous": { + "Positioning mode": "FIX", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Save uncombined": "Off", + "Save single averages": "On", + "AutoAlign": "---", + "Coil Select Mode": "Default" + }, + "System - Adjustments": { + "B0 Shim mode": "Advanced", + "B1 Shim mode": "TrueForm", + "Adj. water suppr.": "On", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "L2.3 A45.1 H61.3 mm", + "Orientation": "C > T-24.6 > S4.6", + "Rotation": "91.26 deg", + "F >> H": "20 mm", + "R >> L": "32 mm", + "A >> P": "34 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249501 MHz", + "Gain": "High", + "Img. Scale Cor.": "1.000", + "Reset": "Off", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "3000 ms" + }, + "Physio - PACE": { + "Resp. control": "Off" + }, + "Sequence - Common": { + "Preparation scans": "4", + "Delta frequency": "-2.3 ppm", + "Ref. scan mode": "Off", + "Phase cycling": "Auto", + "Bandwidth": "2000 Hz", + "Acquisition duration": "1024 ms", + "Remove oversampling": "On" + }, + "Sequence - Special": { + "Inversion Pulse Duration": "9000 us", + "Adiabatic Inversion": "On", + "Inversion Delay": "25000 us", + "Excitation Pulse Duration": "3200 us", + "Refoc Pulse Duration": "8000 us", + "VAPOR water suppression": "On", + "VAPOR Flip Angle": "110 degrees", + "Final VAPOR Delay": "18000 us", + "Additional water suppression": "On" + } + }, + "pages": [ + 16, + 17 + ] + }, + { + "index": 8, + "name": "head_csi_fid", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\head_csi_fid", + "header": { + "ta": "26:36", + "pm": "FIX", + "voxel_size_mm": "50.0×50.0×36.0", + "rel_snr": "1.00", + "sequence": "csi_fid" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'csi_fid' is not a listed Siemens kernel" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "Off", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Rotation": "0 deg", + "Slices": "1", + "VoI A >> P": "400 mm", + "VoI R >> L": "400 mm", + "FoV A >> P": "400 mm", + "FoV R >> L": "400 mm", + "Thickness F >> H": "36 mm", + "TR": "3000 ms", + "TE": "2.3 ms", + "Averages": "60", + "Filter": "None", + "Coil elements": "31P" + }, + "Contrast": { + "TR": "3000 ms", + "TE": "2.3 ms", + "Averages": "60", + "Averaging mode": "Long term", + "Flip angle": "90 deg", + "Water suppr.": "None", + "Measurements": "1" + }, + "Resolution - Common": { + "FoV R >> L": "400 mm", + "FoV A >> P": "400 mm", + "Thickness F >> H": "36 mm", + "Scan res. R >> L": "8", + "Scan res. A >> P": "8", + "Interpol. res. R >> L": "8", + "Interpol. res. A >> P": "8", + "Hamming": "Off", + "Prescan Normalize": "Off", + "Vector size": "512" + }, + "Geometry - Common": { + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Rotation": "0 deg", + "FoV R >> L": "400 mm", + "FoV A >> P": "400 mm", + "Thickness F >> H": "36 mm", + "VoI R >> L": "400 mm", + "VoI A >> P": "400 mm" + }, + "Geometry - AutoAlign": { + "Slice group": "1", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Phase enc. dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "L30.0 A10.7 H24.3", + "L": "30.0 mm", + "A": "10.7 mm", + "H": "24.3 mm", + "Initial Rotation": "0.00 deg", + "Initial Orientation": "T > C", + "T > C": "17.0", + "> S": "0.0" + }, + "System - Miscellaneous": { + "Positioning mode": "FIX", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Save uncombined": "Off", + "AutoAlign": "---", + "Coil Select Mode": "Default" + }, + "System - Adjustments": { + "B0 Shim mode": "Advanced", + "B1 Shim mode": "TrueForm", + "Adj. water suppr.": "Off", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Rotation": "0.00 deg", + "A >> P": "400 mm", + "R >> L": "400 mm", + "F >> H": "36 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm" + }, + "System - Tx/Rx": { + "Frequency 31P": "49.891914 MHz", + "Frequency 1H": "123.249501 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. Scale Cor.": "1.000", + "Reset": "Off", + "? Ref. amplitude 31P": "0.000 V", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "3000 ms" + }, + "Sequence - Common": { + "Preparation scans": "8", + "Dimension": "2D", + "Delta frequency": "0.0 ppm", + "Phase encoding": "Weighted", + "Acquisition delay": "2.3 ms", + "Bandwidth": "4000 Hz", + "Acquisition duration": "128 ms", + "Remove oversampling": "On" + }, + "Sequence - Nuclei": { + "TX/RX Nucleus": "31P", + "TX/RX delta frequency": "0 Hz", + "NOE type": "Rectangular", + "NOE count": "1", + "NOE duration": "5.0 ms", + "NOE flip angle": "90 deg", + "TX Nucleus": "1H", + "TX delta frequency": "0 Hz", + "Decoupling type": "Waltz4", + "Decoupling duration": "1.00 ms", + "DC total duration": "50 %", + "DC pause fract.": "100 %", + "Decoupling flip angle": "180 deg", + "Coil elements": "31P" + } + }, + "pages": [ + 18, + 19 + ] + }, + { + "index": 9, + "name": "head_csi_fid", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\head_csi_fid", + "header": { + "ta": "10:30", + "pm": "FIX", + "voxel_size_mm": "50.0×50.0×40.0", + "rel_snr": "1.00", + "sequence": "csi_fid" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'csi_fid' is not a listed Siemens kernel" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "Off", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Rotation": "0 deg", + "Slices": "1", + "VoI A >> P": "400 mm", + "VoI R >> L": "400 mm", + "FoV A >> P": "400 mm", + "FoV R >> L": "400 mm", + "Thickness F >> H": "40 mm", + "TR": "3000 ms", + "TE": "2.3 ms", + "Averages": "22", + "Filter": "Hamming", + "Coil elements": "31P" + }, + "Contrast": { + "TR": "3000 ms", + "TE": "2.3 ms", + "Averages": "22", + "Averaging mode": "Short term", + "Flip angle": "90 deg", + "Water suppr.": "None", + "Measurements": "1" + }, + "Resolution - Common": { + "FoV R >> L": "400 mm", + "FoV A >> P": "400 mm", + "Thickness F >> H": "40 mm", + "Scan res. R >> L": "8", + "Scan res. A >> P": "8", + "Interpol. res. R >> L": "8", + "Interpol. res. A >> P": "8", + "Hamming": "On", + "Width": "50", + "Prescan Normalize": "Off", + "Vector size": "512" + }, + "Geometry - Common": { + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Rotation": "0 deg", + "FoV R >> L": "400 mm", + "FoV A >> P": "400 mm", + "Thickness F >> H": "40 mm", + "VoI R >> L": "400 mm", + "VoI A >> P": "400 mm" + }, + "Geometry - AutoAlign": { + "Slice group": "1", + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Phase enc. dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "L30.0 A10.7 H24.3", + "L": "30.0 mm", + "A": "10.7 mm", + "H": "24.3 mm", + "Initial Rotation": "0.00 deg", + "Initial Orientation": "T > C", + "T > C": "17.0", + "> S": "0.0" + }, + "System - Miscellaneous": { + "Positioning mode": "FIX", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Save uncombined": "Off", + "AutoAlign": "---", + "Coil Select Mode": "Default" + }, + "System - Adjustments": { + "B0 Shim mode": "Advanced", + "B1 Shim mode": "TrueForm", + "Adj. water suppr.": "Off", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "L30.0 A10.7 H24.3 mm", + "Orientation": "T > C17.0", + "Rotation": "0.00 deg", + "A >> P": "400 mm", + "R >> L": "400 mm", + "F >> H": "40 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm" + }, + "System - Tx/Rx": { + "Frequency 31P": "49.891914 MHz", + "Frequency 1H": "123.249501 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. Scale Cor.": "1.000", + "Reset": "Off", + "? Ref. amplitude 31P": "0.000 V", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "3000 ms" + }, + "Sequence - Common": { + "Preparation scans": "8", + "Dimension": "2D", + "Delta frequency": "0.0 ppm", + "Phase encoding": "Weighted", + "Acquisition delay": "2.3 ms", + "Bandwidth": "4000 Hz", + "Acquisition duration": "128 ms", + "Remove oversampling": "On" + }, + "Sequence - Nuclei": { + "TX/RX Nucleus": "31P", + "TX/RX delta frequency": "0 Hz", + "NOE type": "Rectangular", + "NOE count": "10", + "NOE duration": "5.0 ms", + "NOE pause": "10.0 ms", + "NOE flip angle": "90 deg", + "TX Nucleus": "1H", + "TX delta frequency": "0 Hz", + "Decoupling type": "Waltz4", + "Decoupling duration": "1.00 ms", + "DC total duration": "50 %", + "DC pause fract.": "100 %", + "Decoupling flip angle": "180 deg", + "Coil elements": "31P" + } + }, + "pages": [ + 20, + 21 + ] + }, + { + "index": 10, + "name": "Ax TSE PD T2", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\Ax TSE PD T2", + "header": { + "ta": "3:32", + "pm": "REF", + "voxel_size_mm": "0.4×0.4×4.0", + "pat": "Off", + "rel_snr": "1.00", + "sequence": "tse" + }, + "provenance": { + "verdict": "stock", + "vendor": "Siemens", + "family": "turbo spin echo", + "evidence": [ + "sequence binary 'tse' is a Siemens kernel", + "no sequence-specific parameters printed" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slice group": "1", + "Slices": "30", + "Dist. factor": "25 %", + "Position": "L0.0 P0.0 H0.0 mm", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "AutoAlign": "Head > Brain", + "Phase oversampling": "0 %", + "FoV read": "210 mm", + "FoV phase": "81.3 %", + "Slice thickness": "4.0 mm", + "TR": "3000.0 ms", + "TE 1": "9 ms", + "TE 2": "81 ms", + "Averages": "1", + "Concatenations": "2", + "Filter": "Prescan Normalize", + "Coil elements": "HE1-4" + }, + "Contrast - Common": { + "TR": "3000.0 ms", + "TE 1": "9 ms", + "TE 2": "81 ms", + "TD": "0.0 ms", + "MTC": "Off", + "Magn. preparation": "None", + "Flip angle": "120 deg", + "Fat suppr.": "None", + "Water suppr.": "None", + "Restore magn.": "Off" + }, + "Contrast - Dynamic": { + "Averages": "1", + "Averaging mode": "Long term", + "Reconstruction": "Magnitude", + "Measurements": "1", + "Multiple series": "Each measurement" + }, + "Resolution - Common": { + "FoV read": "210 mm", + "FoV phase": "81.3 %", + "Slice thickness": "4.0 mm", + "Base resolution": "256", + "Phase resolution": "80 %", + "Phase partial Fourier": "Off", + "Trajectory": "Cartesian", + "Interpolation": "On" + }, + "Resolution - iPAT": { + "PAT mode": "None" + }, + "Resolution - Filter Image": { + "Image Filter": "Off", + "Distortion Corr.": "Off", + "Prescan Normalize": "On", + "Unfiltered images": "Off", + "Normalize": "Off", + "B1 filter": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "Off" + }, + "Geometry - Common": { + "Slice group": "1", + "Slices": "30", + "Dist. factor": "25 %", + "Position": "L0.0 P0.0 H0.0 mm", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "FoV read": "210 mm", + "FoV phase": "81.3 %", + "Slice thickness": "4.0 mm", + "TR": "3000.0 ms", + "Multi-slice mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "2" + }, + "Geometry - AutoAlign": { + "Slice group": "1", + "Position": "L0.0 P0.0 H0.0 mm", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "AutoAlign": "Head > Brain", + "Initial Position": "L0.0 P0.0 F37.0", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "37.0 mm", + "Initial Rotation": "90.00 deg", + "Initial Orientation": "Transversal" + }, + "Geometry - Saturation": { + "Fat suppr.": "None", + "Water suppr.": "None", + "Restore magn.": "Off", + "Special sat.": "None" + }, + "Geometry - Navigator": {}, + "System - Miscellaneous": { + "Positioning mode": "REF", + "Table position": "H", + "Table position #2": "37 mm", + "MSMA": "S - 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MB RF pulse BW": "Off", + "SENSE1 coil combine": "Off", + "Invert RO/PE polarity": "On", + "Disable B1 control loop": "Off", + "Disable freq. update": "Off", + "Suppress 16-bit DICOM": "Off", + "Force equal slice timing": "Off", + "Online multi-band recon.": "Online", + "FFT scale factor": "1.00", + "Fat saturation FA": "110.0 deg", + "Fat sat. offset": "0.0 Hz", + "Sinc exc. pulse BWTP": "5.2", + "Physio recording": "File", + "Triggering scheme": "Standard" + } + }, + "pages": [ + 22, + 23 + ] + }, + { + "index": 11, + "name": "SpinEchoFieldMap_AP", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\SpinEchoFieldMap_AP", + "header": { + "ta": "0:32", + "pm": "FIX", + "voxel_size_mm": "2.2×2.2×2.0", + "pat": "Off", + "rel_snr": "1.00", + "sequence": "epse" + }, + "provenance": { + "verdict": "third-party", + "vendor": "CMRR (University of Minnesota)", + "family": "EPI package (C2P), multiband off or not printed", + "signature": "cmrr-epi", + "evidence": [ + "Special card prints SENSE1 coil combine, FFT scale factor, Disable freq. update, Force equal slice timing, Invert RO/PE polarity, Physio recording" + ], + "special_parameters": 13 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "On", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slice group": "1", + "Slices": "72", + "Dist. factor": "0 %", + "Position": "R2.1 A12.6 H7.3 mm", + "Orientation": "T > S1.6 > C0.6", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Phase oversampling": "0 %", + "FoV read": "231 mm", + "FoV phase": "86.5 %", + "Slice thickness": "2.00 mm", + "TR": "8000 ms", + "TE": "66.00 ms", + "Averages": "1", + "Multi-band accel. factor": "1", + "Filter": "None", + "Coil elements": "HC1-7" + }, + "Contrast - Common": { + "TR": "8000 ms", + "TE": "66.00 ms", + "MTC": "Off", + "Magn. preparation": "None", + "Flip angle": "90 deg", + "Refocus flip angle": "180 deg", + "Fat suppr.": "Fat sat.", + "Grad. rev. fat suppr.": "Disabled" + }, + "Contrast - Dynamic": { + "Averages": "1", + "Averaging mode": "Long term", + "Reconstruction": "Magnitude", + "Measurements": "3", + "Delay in TR": "0 ms" + }, + "Resolution - Common": { + "FoV read": "231 mm", + "FoV phase": "86.5 %", + "Slice thickness": "2.00 mm", + "Base resolution": "104", + "Phase resolution": "100 %", + "Phase partial Fourier": "Off", + "Interpolation": "Off" + }, + "Resolution - iPAT": { + "PAT mode": "None" + }, + "Resolution - Filter Image": { + "Distortion Corr.": "Off", + "Prescan Normalize": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "Off", + "Hamming": "Off" + }, + "Geometry - Common": { + "Slice group": "1", + "Slices": "72", + "Dist. factor": "0 %", + "Position": "R2.1 A12.6 H7.3 mm", + "Orientation": "T > S1.6 > C0.6", + "Phase enc. dir.": "A >> P", + "FoV read": "231 mm", + "FoV phase": "86.5 %", + "Slice thickness": "2.00 mm", + "TR": "8000 ms", + "Multi-slice mode": "Interleaved", + "Series": "Interleaved", + "Multi-band accel. factor": "1" + }, + "Geometry - AutoAlign": { + "Slice group": "1", + "Position": "R2.1 A12.6 H7.3 mm", + "Orientation": "T > S1.6 > C0.6", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Rotation": "0.00 deg", + "Initial Orientation": "Transversal" + }, + "Geometry - Saturation": { + "Fat suppr.": "Fat sat.", + "Grad. rev. fat suppr.": "Disabled", + "Special sat.": "None" + }, + "System - Miscellaneous": { + "Positioning mode": "FIX", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combine Mode": "Sum of Squares", + "Matrix Optimization": "Off", + "AutoAlign": "Head > Brain", + "Coil Select Mode": "Off - All" + }, + "System - Adjustments": { + "B0 Shim mode": "Advanced", + "B1 Shim mode": "Patient-specific", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "R2.1 A12.6 H7.3 mm", + "Orientation": "T > S1.6 > C0.6", + "Rotation": "3.04 deg", + "A >> P": "200 mm", + "R >> L": "231 mm", + "F >> H": "144 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "Patient-specific", + "Excitation": "Standard" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249749 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. 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Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "8000 ms", + "Multi-band accel. factor": "1" + }, + "BOLD": { + "GLM Statistics": "Off", + "Dynamic t-maps": "Off", + "Ignore meas. at start": "0", + "Ignore after transition": "0", + "Model transition states": "Off", + "Temp. highpass filter": "Off", + "Threshold": "4.00", + "Paradigm size": "3", + "Meas[1]": "Baseline", + "Meas[2]": "Baseline", + "Meas[3]": "Active", + "Motion correction": "Off", + "Spatial filter": "Off", + "Measurements": "3", + "Delay in TR": "0 ms" + }, + "Sequence - Part 1": { + "Introduction": "Off", + "Dimension": "2D", + "Contrasts": "1", + "Multi-slice mode": "Interleaved", + "Free echo spacing": "On", + "Echo spacing": "0.58 ms", + "Bandwidth": "2290 Hz/Px" + }, + "Sequence - Part 2": { + "EPI factor": "90", + "RF pulse type": "Normal", + "Gradient mode": "Performance", + "Excitation": "Standard" + }, + "Sequence - Special": { + "Min. prep scans": "0", + "Delay before PC scans": "0 us", + "SENSE1 coil combine": "Off", + "Invert RO/PE polarity": "Off", + "Disable B1 control loop": "Off", + "Disable freq. update": "Off", + "Suppress 16-bit DICOM": "Off", + "Force equal slice timing": "Off", + "FFT scale factor": "1.00", + "Fat saturation FA": "110.0 deg", + "Fat sat. offset": "0.0 Hz", + "Physio recording": "Off", + "Triggering scheme": "Standard" + } + }, + "pages": [ + 24, + 25 + ] + }, + { + "index": 12, + "name": "SpinEchoFieldMap_PA", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\SpinEchoFieldMap_PA", + "header": { + "ta": "0:32", + "pm": "FIX", + "voxel_size_mm": "2.2×2.2×2.0", + "pat": "Off", + "rel_snr": "1.00", + "sequence": "epse" + }, + "provenance": { + "verdict": "third-party", + "vendor": "CMRR (University of Minnesota)", + "family": "EPI package (C2P), multiband off or not printed", + "signature": "cmrr-epi", + "evidence": [ + "Special card prints SENSE1 coil combine, FFT scale factor, Disable freq. update, Force equal slice timing, Invert RO/PE polarity, Physio recording" + ], + "special_parameters": 13 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "On", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slice group": "1", + "Slices": "72", + "Dist. factor": "0 %", + "Position": "R2.1 A12.6 H7.3 mm", + "Orientation": "T > S1.6 > C0.6", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Phase oversampling": "0 %", + "FoV read": "231 mm", + "FoV phase": "86.5 %", + "Slice thickness": "2.00 mm", + "TR": "8000 ms", + "TE": "66.00 ms", + "Averages": "1", + "Multi-band accel. factor": "1", + "Filter": "None", + "Coil elements": "HC1-7" + }, + "Contrast - 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Adjust Volume": { + "Position": "R2.1 A12.6 H7.3 mm", + "Orientation": "T > S1.6 > C0.6", + "Rotation": "3.04 deg", + "A >> P": "200 mm", + "R >> L": "231 mm", + "F >> H": "144 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "Patient-specific", + "Excitation": "Standard" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249749 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. 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Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "8000 ms", + "Multi-band accel. factor": "1" + }, + "BOLD": { + "GLM Statistics": "Off", + "Dynamic t-maps": "Off", + "Ignore meas. at start": "0", + "Ignore after transition": "0", + "Model transition states": "Off", + "Temp. highpass filter": "Off", + "Threshold": "4.00", + "Paradigm size": "3", + "Meas[1]": "Baseline", + "Meas[2]": "Baseline", + "Meas[3]": "Active", + "Motion correction": "Off", + "Spatial filter": "Off", + "Measurements": "3", + "Delay in TR": "0 ms" + }, + "Sequence - Part 1": { + "Introduction": "Off", + "Dimension": "2D", + "Contrasts": "1", + "Multi-slice mode": "Interleaved", + "Free echo spacing": "On", + "Echo spacing": "0.58 ms", + "Bandwidth": "2290 Hz/Px" + }, + "Sequence - Part 2": { + "EPI factor": "90", + "RF pulse type": "Normal", + "Gradient mode": "Performance", + "Excitation": "Standard" + }, + "Sequence - Special": { + "Min. prep scans": "0", + "Delay before PC scans": "0 us", + "SENSE1 coil combine": "Off", + "Invert RO/PE polarity": "On", + "Disable B1 control loop": "Off", + "Disable freq. update": "Off", + "Suppress 16-bit DICOM": "Off", + "Force equal slice timing": "Off", + "FFT scale factor": "1.00", + "Fat saturation FA": "110.0 deg", + "Fat sat. offset": "0.0 Hz", + "Physio recording": "Off", + "Triggering scheme": "Standard" + } + }, + "pages": [ + 26, + 27 + ] + }, + { + "index": 13, + "name": "NEW Resting_PA", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\NEW Resting_PA", + "header": { + "ta": "8:05", + "pm": "FIX", + "voxel_size_mm": "2.2×2.2×2.0", + "pat": "Off", + "rel_snr": "1.00", + "sequence": "epfid" + }, + "provenance": { + "verdict": "third-party", + "vendor": "CMRR (University of Minnesota)", + "family": "multiband EPI, BOLD", + "signature": "cmrr-mb-epi-bold", + "evidence": [ + "Special card prints MB LeakBlock kernel, Online multi-band recon." + ], + "special_parameters": 22 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "On", + "Wait for user to start": "On", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slice group": "1", + "Slices": "72", + "Dist. factor": "0 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Phase oversampling": "0 %", + "FoV read": "231 mm", + "FoV phase": "86.5 %", + "Slice thickness": "2.00 mm", + "TR": "800 ms", + "TE": "33.00 ms", + "Averages": "1", + "Multi-band accel. factor": "8", + "Filter": "None", + "Coil elements": "HC2,4,6,7;NC2" + }, + "Contrast - 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Scale Cor.": "1.000", + "Reset": "Off", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "800 ms", + "Multi-band accel. factor": "8" + }, + "BOLD": { + "GLM Statistics": "Off", + "Dynamic t-maps": "Off", + "Ignore meas. at start": "0", + "Ignore after transition": "0", + "Model transition states": "On", + "Temp. highpass filter": "On", + "Threshold": "4.00", + "Paradigm size": "3", + "Meas[1]": "Baseline", + "Meas[2]": "Baseline", + "Meas[3]": "Active", + "Motion correction": "Off", + "Spatial filter": "Off", + "Measurements": "594", + "Delay in TR": "0 ms" + }, + "Sequence - Part 1": { + "Introduction": "Off", + "Dimension": "2D", + "Contrasts": "1", + "Flow comp.": "No", + "Multi-slice mode": "Interleaved", + "Free echo spacing": "Off", + "Echo spacing": "0.58 ms", + "Bandwidth": "2290 Hz/Px" + }, + "Sequence - Part 2": { + "EPI factor": "90", + "Gradient mode": "Performance", + "Excitation": "Standard", + "RF spoiling": "Off" + }, + "Sequence - Special": { + "Excite pulse duration": "6600 us", + "Min. prep scans": "0", + "Min. prep scans SB": "0", + "Delay before PC scans": "0 us", + "Single-band images": "On", + "MB LeakBlock kernel": "On", + "MB dual kernel": "Off", + "MB RF phase scramble": "Off", + "Opt. MB RF pulse BW": "Off", + "SENSE1 coil combine": "Off", + "Invert RO/PE polarity": "On", + "Disable B1 control loop": "Off", + "Disable freq. update": "Off", + "Suppress 16-bit DICOM": "Off", + "Force equal slice timing": "Off", + "Online multi-band recon.": "Online", + "FFT scale factor": "1.00", + "Fat saturation FA": "110.0 deg", + "Fat sat. offset": "0.0 Hz", + "Sinc exc. pulse BWTP": "5.2", + "Physio recording": "File", + "Triggering scheme": "Standard" + } + }, + "pages": [ + 28, + 29 + ] + }, + { + "index": 14, + "name": "T2w_SPC", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\T2w_SPC", + "header": { + "ta": "5:57", + "pm": "FIX", + "voxel_size_mm": "0.8×0.8×0.8", + "pat": "2", + "rel_snr": "1.00", + "sequence": "spc" + }, + "provenance": { + "verdict": "stock", + "vendor": "Siemens", + "family": "SPACE -- 3D turbo spin echo", + "evidence": [ + "sequence binary 'spc' is a Siemens kernel", + "no sequence-specific parameters printed" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "On", + "Wait for user to start": "On", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slab group": "1", + "Slabs": "1", + "Position": "Isocenter", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Phase oversampling": "0 %", + "Slice oversampling": "0.0 %", + "Slices per slab": "208", + "FoV read": "256 mm", + "FoV phase": "93.8 %", + "Slice thickness": "0.80 mm", + "TR": "3200 ms", + "TE": "564 ms", + "Averages": "1.0", + "Concatenations": "1", + "Filter": "Prescan Normalize, Image Filter", + "Coil elements": "HC1-7" + }, + "Contrast - Common": { + "TR": "3200 ms", + "TE": "564 ms", + "MTC": "Off", + "Magn. preparation": "None", + "Fat suppr.": "None", + "Blood suppr.": "Off", + "Restore magn.": "Off" + }, + "Contrast - Dynamic": { + "Averages": "1.0", + "Reconstruction": "Magnitude", + "Measurements": "1", + "Multiple series": "Each measurement" + }, + "Resolution - Common": { + "FoV read": "256 mm", + "FoV phase": "93.8 %", + "Slice thickness": "0.80 mm", + "Base resolution": "320", + "Phase resolution": "100 %", + "Slice resolution": "100 %", + "Phase partial Fourier": "Allowed", + "Slice partial Fourier": "Off", + "Interpolation": "Off" + }, + "Resolution - iPAT": { + "PAT mode": "GRAPPA", + "Accel. factor PE": "2", + "Ref. lines PE": "32", + "Accel. factor 3D": "1", + "Reference scan mode": "Integrated" + }, + "Resolution - Filter Image": { + "Image Filter": "On", + "Intensity": "Sharp", + "Edge Enhancement": "3", + "Smoothing": "3", + "Unfiltered images": "Off", + "Distortion Corr.": "Off", + "Prescan Normalize": "On", + "Unfiltered images #2": "On", + "Normalize": "Off", + "B1 filter": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "Off" + }, + "Geometry - Common": { + "Slab group": "1", + "Slabs": "1", + "Position": "Isocenter", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "Slice oversampling": "0.0 %", + "Slices per slab": "208", + "FoV read": "256 mm", + "FoV phase": "93.8 %", + "Slice thickness": "0.80 mm", + "TR": "3200 ms", + "Series": "Interleaved", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slab group": "1", + "Position": "Isocenter", + "Orientation": "Sagittal", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Rotation": "2.53 deg", + "Initial Orientation": "Sagittal" + }, + "Geometry - Saturation": { + "Fat suppr.": "None", + "Restore magn.": "Off", + "Special sat.": "None" + }, + "Geometry - Navigator": {}, + "System - Miscellaneous": { + "Positioning mode": "FIX", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combine Mode": "Adaptive Combine", + "Save uncombined": "Off", + "Matrix Optimization": "Off", + "AutoAlign": "Head > Brain", + "Coil Select Mode": "Off - All" + }, + "System - Adjustments": { + "B0 Shim mode": "Standard", + "B1 Shim mode": "TrueForm", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "! Position": "Isocenter", + "! Orientation": "Sagittal", + "! Rotation": "0.00 deg", + "! A >> P": "240 mm", + "! F >> H": "256 mm", + "! R >> L": "167 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm", + "Excitation": "Non-sel." + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249749 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. Scale Cor.": "3.000", + "Reset": "Off", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "Trigger delay": "0 ms", + "TR": "3200 ms", + "Concatenations": "1" + }, + "Physio - Cardiac": { + "Magn. preparation": "None", + "Fat suppr.": "None", + "Dark blood": "Off", + "FoV read": "256 mm", + "FoV phase": "93.8 %", + "Phase resolution": "100 %" + }, + "Physio - PACE": { + "Resp. control": "Off", + "Concatenations": "1" + }, + "Inline - Common": { + "Subtract": "Off", + "Measurements": "1", + "StdDev": "Off", + "Save original images": "On" + }, + "Inline - MIP": { + "MIP-Sag": "Off", + "MIP-Cor": "Off", + "MIP-Tra": "Off", + "MIP-Time": "Off", + "Save original images": "On" + }, + "Inline - Composing": { + "Distortion Corr.": "Off" + }, + "Sequence - Part 1": { + "Introduction": "On", + "Dimension": "3D", + "Elliptical scanning": "Off", + "Reordering": "Linear", + "Flow comp.": "No", + "Echo spacing": "3.86 ms", + "Adiabatic-mode": "Off", + "Bandwidth": "744 Hz/Px" + }, + "Sequence - Part 2": { + "Echo train duration": "1166 ms", + "RF pulse type": "Fast", + "Gradient mode": "Fast", + "Excitation": "Non-sel.", + "Flip angle mode": "T2 var", + "Turbo factor": "314" + }, + "Sequence - Assistant": { + "Allowed delay": "0 s" + } + }, + "pages": [ + 30, + 31 + ] + }, + { + "index": 15, + "name": "can_neuromelanin", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\can_neuromelanin", + "header": { + "ta": "8:54", + "pm": "REF", + "voxel_size_mm": "0.4×0.4×1.5", + "pat": "2", + "rel_snr": "1.00", + "sequence": "fl" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'fl' is a Siemens kernel", + "prints 2 sequence-specific parameter(s) no signature accounts for, including MT Flip Angle, MT RF Offset" + ], + "special_parameters": 2 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slice group": "1", + "Slices": "16", + "Dist. factor": "0 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "AutoAlign": "Head > Brain", + "Phase oversampling": "0 %", + "FoV read": "220 mm", + "FoV phase": "75.0 %", + "Slice thickness": "1.5 mm", + "TR": "444.0 ms", + "TE": "4.11 ms", + "Averages": "10", + "Concatenations": "1", + "Filter": "None", + "Coil elements": "HC1-7" + }, + "Contrast - Common": { + "TR": "444.0 ms", + "TE": "4.11 ms", + "MTC": "On", + "Magn. preparation": "None", + "Flip angle": "40 deg", + "Fat suppr.": "None", + "Water suppr.": "None", + "SWI": "Off" + }, + "Contrast - Dynamic": { + "Averages": "10", + "Averaging mode": "Short term", + "Reconstruction": "Magnitude", + "Measurements": "1", + "Multiple series": "Each measurement" + }, + "Resolution - Common": { + "FoV read": "220 mm", + "FoV phase": "75.0 %", + "Slice thickness": "1.5 mm", + "Base resolution": "288", + "Phase resolution": "100 %", + "Phase partial Fourier": "Off", + "Interpolation": "On" + }, + "Resolution - iPAT": { + "PAT mode": "GRAPPA", + "Accel. factor PE": "2", + "Ref. lines PE": "24", + "Reference scan mode": "Integrated" + }, + "Resolution - Filter Image": { + "Image Filter": "Off", + "Distortion Corr.": "Off", + "Prescan Normalize": "Off", + "Normalize": "Off", + "B1 filter": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "Off" + }, + "Geometry - Common": { + "Slice group": "1", + "Slices": "16", + "Dist. factor": "0 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "FoV read": "220 mm", + "FoV phase": "75.0 %", + "Slice thickness": "1.5 mm", + "TR": "444.0 ms", + "Multi-slice mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slice group": "1", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "AutoAlign": "Head > Brain", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Rotation": "90.00 deg", + "Initial Orientation": "Transversal" + }, + "Geometry - Saturation": { + "Saturation mode": "Standard", + "Fat suppr.": "None", + "Water suppr.": "None", + "Special sat.": "None" + }, + "System - Miscellaneous": { + "Positioning mode": "REF", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combine Mode": "Adaptive Combine", + "Save uncombined": "Off", + "Matrix Optimization": "Off", + "AutoAlign": "Head > Brain", + "Coil Select Mode": "Off - All" + }, + "System - Adjustments": { + "B0 Shim mode": "Tune up", + "B1 Shim mode": "TrueForm", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "263 mm", + "R >> L": "350 mm", + "F >> H": "350 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm", + "Excitation": "Slice-sel." + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249749 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. Scale Cor.": "1.000", + "Reset": "Off", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "444.0 ms", + "Concatenations": "1", + "Segments": "1" + }, + "Physio - Cardiac": { + "Magn. preparation": "None", + "Fat suppr.": "None", + "Dark blood": "Off", + "FoV read": "220 mm", + "FoV phase": "75.0 %", + "Phase resolution": "100 %" + }, + "Physio - PACE": { + "Resp. control": "Off", + "Concatenations": "1" + }, + "Inline - Common": { + "Subtract": "Off", + "Measurements": "1", + "StdDev": "Off", + "Liver registration": "Off", + "Save original images": "On" + }, + "Inline - MIP": { + "MIP-Sag": "Off", + "MIP-Cor": "Off", + "MIP-Tra": "Off", + "MIP-Time": "Off", + "Save original images": "On" + }, + "Inline - Soft Tissue": { + "Wash - In": "Off", + "Wash - Out": "Off", + "TTP": "Off", + "PEI": "Off", + "MIP - time": "Off", + "Measurements": "1" + }, + "Inline - Composing": { + "Distortion Corr.": "Off" + }, + "Sequence - Part 1": { + "Introduction": "On", + "Dimension": "2D", + "Phase stabilisation": "Off", + "Asymmetric echo": "Off", + "Contrasts": "1", + "Flow comp.": "No", + "Multi-slice mode": "Interleaved", + "Bandwidth": "390 Hz/Px" + }, + "Sequence - Part 2": { + "Segments": "1", + "Acoustic noise reduction": "None", + "RF pulse type": "Normal", + "Gradient mode": "Fast", + "Excitation": "Slice-sel.", + "RF spoiling": "On" + }, + "Sequence - Special": { + "MT Flip Angle": "300", + "MT RF Offset": "1200" + }, + "Sequence - Assistant": { + "Mode": "Off", + "Allowed delay": "0 s" + } + }, + "pages": [ + 32, + 33 + ] + }, + { + "index": 16, + "name": "dMRI_dir64_MGH_AP_b0N5", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\dMRI_dir64_MGH_AP_b0N5", + "header": { + "ta": "4:01", + "pm": "FIX", + "voxel_size_mm": "1.5×1.5×1.5", + "pat": "Off", + "rel_snr": "1.00", + "sequence": "epse" + }, + "provenance": { + "verdict": "third-party", + "vendor": "CMRR (University of Minnesota)", + "family": "multiband EPI, diffusion", + "signature": "cmrr-mb-epi-diffusion", + "evidence": [ + "Special card prints MB LeakBlock kernel, Online multi-band recon." + ], + "special_parameters": 21 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "On", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slice group": "1", + "Slices": "92", + "Dist. factor": "0 %", + "Position": "L0.0 A1.9 H2.6 mm", + "Orientation": "T > C-20.0", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Phase oversampling": "0 %", + "FoV read": "210 mm", + "FoV phase": "100.0 %", + "Slice thickness": "1.50 mm", + "TR": "3230 ms", + "TE": "89.20 ms", + "Multi-band accel. factor": "4", + "Filter": "None", + "Coil elements": "HC1-7;NC1,2" + }, + "Contrast - Common": { + "TR": "3230 ms", + "TE": "89.20 ms", + "MTC": "Off", + "Magn. preparation": "None", + "Flip angle": "78 deg", + "Refocus flip angle": "160 deg", + "Fat suppr.": "None", + "Grad. rev. fat suppr.": "Enabled" + }, + "Contrast - Dynamic": { + "Averaging mode": "Long term", + "Reconstruction": "Magnitude", + "Measurements": "1", + "Delay in TR": "0 ms", + "Multiple series": "Off" + }, + "Resolution - Common": { + "FoV read": "210 mm", + "FoV phase": "100.0 %", + "Slice thickness": "1.50 mm", + "Base resolution": "140", + "Phase resolution": "100 %", + "Phase partial Fourier": "6/8", + "Interpolation": "Off" + }, + "Resolution - iPAT": { + "PAT mode": "None" + }, + "Resolution - Filter Image": { + "Distortion Corr.": "Off", + "Prescan Normalize": "Off", + "Dynamic Field Corr.": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "Off" + }, + "Geometry - Common": { + "Slice group": "1", + "Slices": "92", + "Dist. factor": "0 %", + "Position": "L0.0 A1.9 H2.6 mm", + "Orientation": "T > C-20.0", + "Phase enc. dir.": "A >> P", + "FoV read": "210 mm", + "FoV phase": "100.0 %", + "Slice thickness": "1.50 mm", + "TR": "3230 ms", + "Multi-slice mode": "Interleaved", + "Series": "Interleaved", + "Multi-band accel. factor": "4" + }, + "Geometry - AutoAlign": { + "Slice group": "1", + "Position": "L0.0 A1.9 H2.6 mm", + "Orientation": "T > C-20.0", + "Phase enc. dir.": "A >> P", + "AutoAlign": "Head > Brain", + "Initial Position": "L0.0 A1.9 H2.6", + "R": "0.0 mm", + "A": "1.9 mm", + "H": "2.6 mm", + "Initial Rotation": "0.00 deg", + "Initial Orientation": "T > C", + "T > C": "-20.0", + "> S": "0.0" + }, + "Geometry - Saturation": { + "Fat suppr.": "None", + "Grad. rev. fat suppr.": "Enabled", + "Special sat.": "None" + }, + "Geometry - Navigator": {}, + "System - Miscellaneous": { + "Positioning mode": "FIX", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combine Mode": "Sum of Squares", + "Matrix Optimization": "Off", + "AutoAlign": "Head > Brain", + "Coil Select Mode": "Off - All" + }, + "System - Adjustments": { + "B0 Shim mode": "Standard", + "B1 Shim mode": "TrueForm", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "L0.0 A1.9 H2.6 mm", + "Orientation": "T > C-20.0", + "Rotation": "0.00 deg", + "A >> P": "210 mm", + "R >> L": "210 mm", + "F >> H": "138 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm", + "Excitation": "Standard" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249749 MHz", + "Correction factor": "1", + "Gain": "High", + "Img. Scale Cor.": "1.000", + "Reset": "Off", + "? Ref. amplitude 1H": "0.000 V" + }, + "Physio - Signal1": { + "1st Signal/Mode": "None", + "TR": "3230 ms", + "Multi-band accel. factor": "4" + }, + "Physio - PACE": { + "Resp. control": "Off", + "Multi-band accel. factor": "4" + }, + "Diff - Neuro": { + "Diffusion mode": "MDDW", + "Diff. directions": "64", + "Diffusion Scheme": "Monopolar", + "Diff. weightings": "2", + "b-value 1": "0 s/mm²", + "b-value 2": "2000 s/mm²", + "b-value 1 #2": "5", + "b-value 2 #2": "1", + "Diff. weighted images": "On", + "Trace weighted images": "On", + "ADC maps": "On", + "FA maps": "On", + "Mosaic": "On", + "Tensor": "On", + "Noise level": "40" + }, + "Diff - Body": { + "Diffusion mode": "MDDW", + "Diff. directions": "64", + "Diffusion Scheme": "Monopolar", + "Diff. weightings": "2", + "b-value 1": "0 s/mm²", + "b-value 2": "2000 s/mm²", + "b-value 1 #2": "5", + "b-value 2 #2": "1", + "Diff. weighted images": "On", + "Trace weighted images": "On", + "ADC maps": "On", + "Exponential ADC Maps": "Off", + "FA maps": "On", + "Invert Gray Scale": "Off", + "Calculated Image": "Off", + "b-Value >=": "0 s/mm²", + "Noise level": "40" + }, + "Diff - Composing": { + "Distortion Corr.": "Off" + }, + "Sequence - Part 1": { + "Introduction": "On", + "Dimension": "2D", + "Multi-slice mode": "Interleaved", + "Free echo spacing": "Off", + "Echo spacing": "0.69 ms", + "Bandwidth": "1700 Hz/Px" + }, + "Sequence - Part 2": { + "EPI factor": "140", + "Gradient mode": "Performance", + "Excitation": "Standard", + "RF spoiling": "Off" + }, + "Sequence - Special": { + "Excite pulse duration": "3840 us", + "Refocus pulse duration": "7680 us", + "Min. prep scans": "0", + "Min. prep scans SB": "0", + "Delay before PC scans": "0 us", + "Single-band images": "On", + "MB LeakBlock kernel": "On", + "MB dual kernel": "Off", + "MB RF phase scramble": "Off", + "Opt. 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Ref. amplitude 1H": "0.000 V" + }, + "Sequence - Common": { + "Preparation scans": "10", + "Dimension": "3D", + "Delta frequency": "-2.40 ppm", + "Phase encoding": "Full", + "Acquisition delay": "2.3 ms", + "Bandwidth": "167000 Hz", + "Acquisition duration": "0 ms", + "Remove oversampling": "Off" + }, + "Sequence - Nuclei": { + "TX/RX Nucleus": "1H", + "TX/RX delta frequency": "0 Hz", + "TX Nucleus": "None", + "TX delta frequency": "0 Hz", + "Coil elements": "HE1-4" + }, + "Sequence - Special": { + "PE Samp EPSI": "SegsGS_216x108_Ry3B143_SyV60.dat", + "PE Samp EBSI": "No Customized Sampling Pattern", + "PE Samp DEPI": "No Customized Sampling Pattern", + "Mode: DEPInav": "0 #", + "Mode: DEPIref": "0 #", + "Mode: MotionNav": "60 #", + "Mode: WatSupNav": "1 #", + "Mode: BipolNav": "1 #", + "Mode: RFspoil": "0 #", + "Ramping time (PE)": "180 us", + "Grad duration (PE)": "480 us", + "Blip ramp time (PE)": "60 us", + "Blip ramp time (SL)": "60 us", + "Jump ramp time (JP)": "170 us", + "Jump flat time (JP)": "200 us", + "Ramping time (SP)": "180 us", + "Spoil duration (SP)": "4000 us", + "Spoil amplitude(SP)": "20 mT/mm", + "EPSI. 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Echo Pair": "10 #" + } + }, + "pages": [ + 38, + 39 + ] + }, + { + "index": 19, + "name": "ZPL_RG_EPSI_FID_v2e_FeiDu", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\ZPL_RG_EPSI_FID_v2e_FeiDu", + "header": { + "ta": "1:32", + "pm": "FIX", + "voxel_size_mm": "1.1×1.0×1.7", + "rel_snr": "1.00", + "sequence": "ZPL_epsi_fid" + }, + "provenance": { + "verdict": "third-party", + "vendor": "UIUC (Zhi-Pei Liang)", + "family": "SPICE -- spectroscopic imaging by exploiting spatiospectral correlation", + "signature": "spice-epsi", + "evidence": [ + "sequence binary 'ZPL_epsi_fid'", + "Special card prints PE Samp EPSI, EPSI. 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BlipLeng: Phas": "256 #", + "EPSI. BlipStep: Phas": "3 #", + "EPSI. BlipStep: Slic": "1 #", + "EPSI. Ramp. Samp": "16 #", + "EPSI. RO. Ramp time": "110 us", + "EPSI. EchoSpace": "3200 us", + "T2Prep. Echo time": "100000 us", + "T2Prep. Pulse mode": "1 #", + "Prep. 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EPSI" + ], + "special_parameters": 54 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0 deg", + "Slabs": "1", + "VoI A >> P": "240 mm", + "VoI R >> L": "240 mm", + "VoI F >> H": "100 mm", + "FoV A >> P": "240 mm", + "FoV R >> L": "240 mm", + "FoV F >> H": "120 mm", + "TR": "800 ms", + "TE": "1.6 ms", + "Averages": "1", + "Filter": "None", + "Coil elements": "HE1-4" + }, + "Contrast": { + "TR": "800 ms", + "TE": "1.6 ms", + "Ernst angle": "56 deg", + "WaterSupp Angle": "90 deg", + "FOV Pos, Read": "0 um", + "FOV Pos, Phase": "0 um", + "FOV Pos, Slice": "0 um", + "Averages": "1", + "Averaging mode": "Short term", + "Flip angle": "90 deg", + "Water suppr.": "Water sat.", + "Water suppr. 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TR": "350.0 ms", + "Allowed delay": "60 s" + } + }, + "pages": [ + 44, + 45 + ] + }, + { + "index": 22, + "name": "flash3d_FOV120_FA4", + "path": "\\\\Research\\Investigators\\FeiDu\\BEEST_SPICE_11112025\\flash3d_FOV120_FA4", + "header": { + "ta": "0:20", + "pm": "FIX", + "voxel_size_mm": "1.5×1.5×3.0", + "pat": "3", + "rel_snr": "1.00", + "sequence": "fl" + }, + "provenance": { + "verdict": "stock", + "vendor": "Siemens", + "family": "FLASH -- spoiled gradient echo", + "evidence": [ + "sequence binary 'fl' is a Siemens kernel", + "no sequence-specific parameters printed" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Prio recon": "Off", + "Load images to viewer": "On", + "Inline movie": "Off", + "Auto store images": "On", + "Load images to stamp segments": "Off", + "Load images to graphic segments": "Off", + "Auto open inline display": "Off", + "Auto close inline display": "Off", + "Start measurement without further preparation": "Off", + "Wait for user to start": "Off", + "Start measurements": "Single measurement" + }, + "Routine": { + "Slab group": "1", + "Slabs": "1", + "Dist. factor": "20 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "AutoAlign": "---", + "Phase oversampling": "0 %", + "Slice oversampling": "20.0 %", + "Slices per slab": "40", + "FoV read": "240 mm", + "FoV phase": "100.0 %", + "Slice thickness": "3.00 mm", + "TR": "5.0 ms", + "TE": "2.20 ms", + "Averages": "1", + "Concatenations": "1", + "Filter": "Prescan Normalize, Elliptical filter", + "Coil elements": "HE1-4" + }, + "Contrast - Common": { + "TR": "5.0 ms", + "TE": "2.20 ms", + "MTC": "Off", + "Magn. preparation": "None", + "Flip angle": "4 deg", + "Fat suppr.": "None", + "Water suppr.": "None", + "SWI": "Off" + }, + "Contrast - Dynamic": { + "Averages": "1", + "Averaging mode": "Long term", + "Reconstruction": "Magnitude", + "Measurements": "1", + "Multiple series": "Each measurement" + }, + "Resolution - Common": { + "FoV read": "240 mm", + "FoV phase": "100.0 %", + "Slice thickness": "3.00 mm", + "Base resolution": "160", + "Phase resolution": "100 %", + "Slice resolution": "100 %", + "Phase partial Fourier": "Off", + "Slice partial Fourier": "Off", + "Interpolation": "Off" + }, + "Resolution - iPAT": { + "PAT mode": "GRAPPA", + "Accel. factor PE": "3", + "Ref. lines PE": "36", + "Accel. factor 3D": "1", + "Reference scan mode": "Integrated" + }, + "Resolution - Filter Image": { + "Image Filter": "Off", + "Distortion Corr.": "Off", + "Prescan Normalize": "On", + "Unfiltered images": "Off", + "Normalize": "Off", + "B1 filter": "Off" + }, + "Resolution - Filter Rawdata": { + "Raw filter": "Off", + "Elliptical filter": "On" + }, + "Geometry - Common": { + "Slab group": "1", + "Slabs": "1", + "Dist. factor": "20 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "Slice oversampling": "20.0 %", + "Slices per slab": "40", + "FoV read": "240 mm", + "FoV phase": "100.0 %", + "Slice thickness": "3.00 mm", + "TR": "5.0 ms", + "Multi-slice mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slab group": "1", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase enc. dir.": "R >> L", + "AutoAlign": "---", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Rotation": "90.00 deg", + "Initial Orientation": "Transversal" + }, + "Geometry - Saturation": { + "Saturation mode": "Standard", + "Fat suppr.": "None", + "Water suppr.": "None", + "Special sat.": "None" + }, + "System - Miscellaneous": { + "Positioning mode": "FIX", + "Table position": "H", + "Table position #2": "0 mm", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combine Mode": "Adaptive Combine", + "Save uncombined": "Off", + "Matrix Optimization": "Off", + "AutoAlign": "---", + "Coil Select Mode": "Off - AutoCoilSelect" + }, + "System - Adjustments": { + "B0 Shim mode": "Standard", + "B1 Shim mode": "TrueForm", + "Adjust with body coil": "Off", + "Confirm freq. adjustment": "Off", + "Assume Dominant Fat": "Off", + "Assume Silicone": "Off", + "Adjustment Tolerance": "Auto" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "90.00 deg", + "R >> L": "240 mm", + "A >> P": "240 mm", + "F >> H": "120 mm", + "Reset": "Off" + }, + "System - pTx Volumes": { + "B1 Shim mode": "TrueForm", + "Excitation": "Slab-sel." + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249749 MHz", + "Correction factor": "1", + "Gain": "Low", + "Img. 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BW": "35 Hz", + "Spectral Suppr.": "None" + }, + "Resolution - Common": { + "Vector Size": "2048", + "Normalize": "Off" + }, + "Geometry - Common": { + "Position": "Isocenter", + "Orientation": "C > T-24.6 > S4.6", + "Rotation": "1.26 deg", + "VoI R >> L": "32 mm", + "VoI F >> H": "20 mm", + "VoI A >> P": "34 mm" + }, + "Geometry - AutoAlign": { + "AutoAlign": "---", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "Geometry - Navigator": {}, + "System - Miscellaneous": { + "Coil Selection": "Auto Coil Select", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Tune up", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off", + "Adj. Water Suppr.": "On" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "C > T-24.6 > S4.6", + "Rotation": "91.26 deg", + "F >> H": "20 mm", + "R >> L": "32 mm", + "A >> P": "34 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249491 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "3000.0 ms" + }, + "Physio - PACE": { + "Resp. Control": "Off" + }, + "Sequence - Common": { + "Sequence Name": "svs_se", + "Preparation Scans": "4", + "Delta Frequency": "0.00 ppm", + "Ref. Scan Mode": "Off", + "Measurements": "1", + "Phase Cycling": "Auto", + "Save Uncombined": "Off", + "Bandwidth": "1000 Hz", + "Acquisition Duration": "2048 ms", + "Remove Oversampling": "On", + "Freq. Corr. Accumulation": "Off", + "Incr. Gradient Spoiling": "Off" + } + }, + "pages": [ + 18, + 19 + ] + }, + { + "index": 8, + "name": "head_csi_fid", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\head_csi_fid", + "header": { + "ta": "12:54 min", + "coil_selection": "Auto", + "voxel_size_mm": "25.0×25.0×25.0", + "rel_snr": "1.00", + "sequence": "csi_fid" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'csi_fid' is not a listed Siemens kernel" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "Off", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "FOV A >> P": "400 mm", + "FOV R >> L": "400 mm", + "Thickness F >> H": "25 mm", + "VoI A >> P": "400 mm", + "VoI R >> L": "400 mm", + "TR": "1500.0 ms", + "TE": "2.30 ms", + "Averages": "2" + }, + "Contrast - Common": { + "TR": "1500.0 ms", + "TE": "2.30 ms", + "Flip Angle": "90 deg", + "Preparation Scans": "4", + "Averages": "2", + "Water Suppression": "Water Saturation", + "Water Suppr. BW": "35 Hz" + }, + "Resolution - Common": { + "FOV A >> P": "400 mm", + "FOV R >> L": "400 mm", + "Thickness F >> H": "25 mm", + "Scan Res. A >> P": "16", + "Scan Res. R >> L": "16", + "Interpol. Res. A >> P": "16", + "Interpol. Res. R >> L": "16", + "Hamming": "Off", + "Dimension": "2D", + "Phase Encoding": "Full", + "Vector Size": "512", + "Normalize": "Off" + }, + "Geometry - Common": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "FOV A >> P": "400 mm", + "FOV R >> L": "400 mm", + "Thickness F >> H": "25 mm", + "VoI A >> P": "400 mm", + "VoI R >> L": "400 mm" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "System - Miscellaneous": { + "Coil Selection": "Auto Coil Select", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Tune up", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off", + "Adj. Water Suppr.": "On" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "400 mm", + "R >> L": "400 mm", + "F >> H": "25 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249491 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "1500.0 ms" + }, + "Sequence - Common": { + "Sequence Name": "csi_fid", + "Preparation Scans": "4", + "Delta Frequency": "0.00 ppm", + "Measurements": "1", + "Dimension": "2D", + "Save Uncombined": "Off", + "Acquisition Delay": "2.30 ms", + "Bandwidth": "1000 Hz", + "Acquisition Duration": "512 ms", + "Remove Oversampling": "On" + }, + "Sequence - Nuclei": { + "TX/RX Nucleus": "1H", + "TX/RX Delta Frequency": "0 Hz", + "NOE Type": "None", + "TX Nucleus": "None", + "TX Delta Frequency": "0 Hz", + "Decoupling Type": "None" + } + }, + "pages": [ + 20, + 21 + ] + }, + { + "index": 9, + "name": "head_csi_fid", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\head_csi_fid", + "header": { + "ta": "12:54 min", + "coil_selection": "Auto", + "voxel_size_mm": "25.0×25.0×25.0", + "rel_snr": "1.00", + "sequence": "csi_fid" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'csi_fid' is not a listed Siemens kernel" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "Off", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "FOV A >> P": "400 mm", + "FOV R >> L": "400 mm", + "Thickness F >> H": "25 mm", + "VoI A >> P": "400 mm", + "VoI R >> L": "400 mm", + "TR": "1500.0 ms", + "TE": "2.30 ms", + "Averages": "2" + }, + "Contrast - Common": { + "TR": "1500.0 ms", + "TE": "2.30 ms", + "Flip Angle": "90 deg", + "Preparation Scans": "4", + "Averages": "2", + "Water Suppression": "Water Saturation", + "Water Suppr. BW": "35 Hz" + }, + "Resolution - Common": { + "FOV A >> P": "400 mm", + "FOV R >> L": "400 mm", + "Thickness F >> H": "25 mm", + "Scan Res. A >> P": "16", + "Scan Res. R >> L": "16", + "Interpol. Res. A >> P": "16", + "Interpol. Res. R >> L": "16", + "Hamming": "Off", + "Dimension": "2D", + "Phase Encoding": "Full", + "Vector Size": "512", + "Normalize": "Off" + }, + "Geometry - Common": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "FOV A >> P": "400 mm", + "FOV R >> L": "400 mm", + "Thickness F >> H": "25 mm", + "VoI A >> P": "400 mm", + "VoI R >> L": "400 mm" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "System - Miscellaneous": { + "Coil Selection": "Auto Coil Select", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Tune up", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off", + "Adj. Water Suppr.": "On" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "400 mm", + "R >> L": "400 mm", + "F >> H": "25 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249491 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "1500.0 ms" + }, + "Sequence - Common": { + "Sequence Name": "csi_fid", + "Preparation Scans": "4", + "Delta Frequency": "0.00 ppm", + "Measurements": "1", + "Dimension": "2D", + "Save Uncombined": "Off", + "Acquisition Delay": "2.30 ms", + "Bandwidth": "1000 Hz", + "Acquisition Duration": "512 ms", + "Remove Oversampling": "On" + }, + "Sequence - Nuclei": { + "TX/RX Nucleus": "1H", + "TX/RX Delta Frequency": "0 Hz", + "NOE Type": "None", + "TX Nucleus": "None", + "TX Delta Frequency": "0 Hz", + "Decoupling Type": "None" + } + }, + "pages": [ + 22, + 23 + ] + }, + { + "index": 10, + "name": "Ax TSE PD T2", + "path": "\\\\Research\\Investigators\\XChen\\31P CSI 20230503 NOE\\Ax TSE PD T2", + "header": { + "ta": "3:32 min", + "coil_selection": "Auto", + "voxel_size_mm": "0.4×0.4×4.0", + "pat": "None", + "rel_snr": "1.00", + "sequence": "tse" + }, + "provenance": { + "verdict": "stock", + "vendor": "Siemens", + "family": "turbo spin echo", + "evidence": [ + "sequence binary 'tse' is a Siemens kernel", + "no sequence-specific parameters printed" + ], + "special_parameters": 0 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "Off", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Slice Group": "1", + "Slices": "30", + "Distance Factor": "25 %", + "Position": "L0.0 P0.0 H0.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "R >> L", + "Phase Oversampling": "0 %", + "FOV Read": "210 mm", + "FOV Phase": "81.3 %", + "Slice Thickness": "4.0 mm", + "TR": "3000.0 ms", + "TE 1": "9.00 ms", + "TE 2": "81.00 ms", + "Averages": "1", + "Concatenations": "2", + "AutoAlign": "Head > Brain" + }, + "Contrast - Common": { + "TR": "3000.0 ms", + "TE 1": "9.00 ms", + "TE 2": "81.00 ms", + "TD": "0.00 ms", + "MTC": "Off", + "Magn. Preparation": "None", + "Flip Angle Mode": "Constant", + "Flip Angle": "120 deg", + "Fat-Water Contrast": "Standard", + "Dark Blood": "Off", + "Contrasts": "2", + "Wrap-up Magn.": "None", + "Reconstruction": "Magnitude" + }, + "Contrast - Dynamic": { + "Dynamic Mode": "Standard", + "Measurements": "1", + "Multiple Series": "Each Measurement" + }, + "Resolution - Common": { + "FOV Read": "210 mm", + "FOV Phase": "81.3 %", + "Slice Thickness": "4.0 mm", + "Base Resolution": "256", + "Phase Resolution": "80 %", + "Interpolation": "On" + }, + "Resolution - Acceleration": { + "Acceleration Mode": "None", + "Deep Resolve": "Off", + "Phase Partial Fourier": "Off" + }, + "Resolution - Filter": { + "Raw Filter": "Off", + "Elliptical Filter": "Off", + "Distortion Correction": "2D", + "Normalize": "Prescan", + "Image Filter": "Off" + }, + "Geometry - Common": { + "Slice Group": "1", + "Slices": "30", + "Distance Factor": "25 %", + "Position": "L0.0 P0.0 H0.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "R >> L", + "Phase Oversampling": "0 %", + "FOV Read": "210 mm", + "FOV Phase": "81.3 %", + "Slice Thickness": "4.0 mm", + "TR": "3000.0 ms", + "Multi-Slice Mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "2" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "L0.0 P0.0 H0.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "R >> L", + "AutoAlign": "Head > Brain", + "Initial Position": "L0.0 P0.0 F37.0", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "37.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "90.00 deg" + }, + "Geometry - Navigator": {}, + "Geometry - Saturation": { + "Special Saturation": "None" + }, + "Geometry - Tim Planning Suite": { + "Set-n-Go Protocol": "Off", + "Table Position": "37 mm", + "Table Position #2": "H", + "Inline Composing": "Off" + }, + "System - Miscellaneous": { + "Coil Selection": "ACS All but spine", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combination": "Adaptive Combine", + "Matrix Optimization": "Off", + "Coil Focus": "Flat" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Standard", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off" + }, + "System - Adjust Volume": { + "Position": "L0.0 P0.0 H0.0 mm", + "Orientation": "Transversal", + "Rotation": "90.00 deg", + "R >> L": "171 mm", + "A >> P": "210 mm", + "F >> H": "149 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm", + "LR Balancing": "Off" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249491 MHz", + "? 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Highpass Filter": "On", + "Threshold": "4.00", + "Paradigm Size": "3", + "Meas[1]": "Baseline", + "Meas[2]": "Baseline", + "Meas[3]": "Active", + "Motion Correction": "Off", + "Spatial Filter": "Off", + "Measurements": "383", + "Delay in TR": "0.00 ms" + }, + "Sequence - Part 1": { + "Sequence Name": "epfid", + "Dimension": "2D", + "Excitation": "Standard", + "Gradient Mode": "Performance", + "Flow Compensation": "None", + "Bandwidth": "2778 Hz/Px", + "Echo Spacing": "0.49 ms", + "Free Echo Spacing": "Off", + "EPI Factor": "90" + }, + "Sequence - Part 2": { + "Introduction": "Off", + "RF Spoiling": "Off" + }, + "Sequence - Special": { + "Excite pulse duration": "5960 us", + "Min. prep scans": "0", + "Min. prep scans SB": "0", + "Delay before PC scans": "0 us", + "Single-band images": "On", + "MB LeakBlock kernel": "On", + "MB dual kernel": "Off", + "MB RF phase scramble": "Off", + "Opt. MB RF pulse BW": "Off", + "SENSE1 coil combine": "Off", + "Invert RO/PE polarity": "On", + "Disable freq. update": "Off", + "Suppress 16-bit DICOM": "Off", + "Force equal slice timing": "Off", + "Online multi-band recon.": "Online", + "FFT scale factor": "1.00", + "Physio recording": "Off", + "Triggering scheme": "Standard" + }, + "Sequence - Assistant": { + "SAR Assistant": "Off" + } + }, + "pages": [ + 38, + 39 + ] + }, + { + "index": 16, + "name": "ABCD_fMRI_rest_MGH", + "path": "\\\\Research\\Investigators\\Frederick\\Potpourri_P1\\ABCD_fMRI_rest_MGH", + "header": { + "ta": "5:14 min", + "coil_selection": "Auto", + "voxel_size_mm": "2.4×2.4×2.4", + "pat": "12", + "rel_snr": "1.00", + "sequence": "epfid" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'epfid' is a Siemens kernel", + "prints 10 sequence-specific parameter(s) no signature accounts for, including ACS mode, CC Mode, FLEET Dummy Pulses" + ], + "special_parameters": 10 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "Off", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Slice Group": "1", + "Slices": "60", + "Distance Factor": "0 %", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "TR": "800.0 ms", + "TE": "30.00 ms", + "Averages": "1", + "Concatenations": "1", + "AutoAlign": "---" + }, + "Contrast - Common": { + "TR": "800.0 ms", + "TE": "30.00 ms", + "MTC": "Off", + "Flip Angle": "90 deg", + "Fat-Water Contrast": "Fat Saturation", + "Reconstruction": "Magnitude" + }, + "Contrast - Dynamic": { + "Dynamic Mode": "Standard", + "Measurements": "383", + "Delay in TR": "0.00 ms" + }, + "Resolution - Common": { + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "Base Resolution": "90", + "Phase Resolution": "100 %", + "Interpolation": "Off" + }, + "Resolution - Acceleration": { + "Acceleration Mode": "SMS", + "Reference Scans": "EPI/Separate", + "Acceleration Factor PE": "2", + "Reference Lines PE": "44", + "SMS Factor": "6", + "FOV Shift Factor": "2", + "Phase Partial Fourier": "Off" + }, + "Resolution - Filter": { + "Raw Filter": "Off", + "Elliptical Filter": "Off", + "Hamming": "Off", + "Distortion Correction": "2D", + "Static Field Correction": "Off", + "Normalize": "Off" + }, + "Geometry - Common": { + "Slice Group": "1", + "Slices": "60", + "Distance Factor": "0 %", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "TR": "800.0 ms", + "Multi-Slice Mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "L0.0 P8.0 H6.0", + "L": "0.0 mm", + "P": "8.0 mm", + "H": "6.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "Geometry - Saturation": { + "Special Saturation": "None" + }, + "Geometry - Tim Planning Suite": { + "Set-n-Go Protocol": "Off", + "Table Position": "6 mm", + "Table Position #2": "H", + "Inline Composing": "Off" + }, + "System - Miscellaneous": { + "Coil Selection": "Auto Coil Select", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combination": "Sum of Squares", + "Matrix Optimization": "Off", + "Coil Focus": "Flat" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Standard", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off" + }, + "System - Adjust Volume": { + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "216 mm", + "R >> L": "216 mm", + "F >> H": "144 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm", + "Excitation": "Standard" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249549 MHz", + "? 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Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "285.0 ms", + "Concatenations": "1" + }, + "Inline - Subtraction": { + "Subtract": "Off", + "Measurements": "1", + "StdDev": "Off", + "Save Original Images": "On" + }, + "Inline - MIP": { + "MIP Sag": "Off", + "MIP Cor": "Off", + "MIP Tra": "Off", + "MIP Time": "Off", + "Radial MIP": "Off", + "Save Original Images": "On", + "MPR Sag": "Off", + "MPR Cor": "Off", + "MPR Tra": "Off" + }, + "Inline - Composing": { + "Inline Composing": "Off" + }, + "Sequence - Part 1": { + "Sequence Name": "epse", + "Excitation": "Standard", + "RF Pulse Type": "Normal", + "Gradient Mode": "Fast", + "Bandwidth": "752 Hz/Px", + "Echo Spacing": "1.38 ms", + "Free Echo Spacing": "Off", + "EPI Factor": "128" + }, + "Sequence - Part 2": { + "Introduction": "Off" + }, + "Sequence - Special": { + "Imaging Dummy TRs": "-1", + "SMS ACS Dummy TRs": "-1", + "FLEET Dummy Pulses": "0", + "RF Clip": "0", + "VERSE Factor": "1.00", + "ACS mode": "Standard", + "Kernel Size": "3x3", + "Wait for TCP/IP Trigger": "Off", + "Reverse Phase Encoding": "Off" + }, + "Sequence - Assistant": { + "SAR Assistant": "Off" + } + }, + "pages": [ + 36, + 37 + ] + }, + { + "index": 15, + "name": "ABCD_fMRI_rest_CMRR", + "path": "\\\\Research\\Investigators\\Frederick\\Potpourri_P1_changed\\ABCD_fMRI_rest_CMRR", + "header": { + "ta": "5:14 min", + "coil_selection": "Manual", + "voxel_size_mm": "2.4×2.4×2.4", + "pat": "None", + "rel_snr": "1.00", + "sequence": "epfid" + }, + "provenance": { + "verdict": "third-party", + "vendor": "CMRR (University of Minnesota)", + "family": "multiband EPI, BOLD", + "signature": "cmrr-mb-epi-bold", + "evidence": [ + "Special card prints MB LeakBlock kernel, Online multi-band recon." + ], + "special_parameters": 18 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "Off", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Slice Group": "1", + "Slices": "60", + "Distance Factor": "0 %", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "TR": "800.0 ms", + "TE": "30.00 ms", + "Averages": "1", + "Multi-band accel. factor": "6", + "AutoAlign": "---", + "Coil Elements": "HC1-7" + }, + "Contrast - Common": { + "TR": "800.0 ms", + "TE": "30.00 ms", + "MTC": "Off", + "Magn. Preparation": "None", + "Flip Angle": "52 deg", + "Fat-Water Contrast": "Fat Saturation", + "Contrasts": "1", + "Reconstruction": "Magnitude" + }, + "Contrast - Dynamic": { + "Dynamic Mode": "Standard", + "Measurements": "383", + "Delay in TR": "0.00 ms" + }, + "Resolution - Common": { + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "Base Resolution": "90", + "Phase Resolution": "100 %", + "Interpolation": "Off" + }, + "Resolution - Acceleration": { + "Acceleration Mode": "None", + "Phase Partial Fourier": "Off" + }, + "Resolution - Filter": { + "Raw Filter": "Off", + "Elliptical Filter": "Off", + "Hamming": "Off", + "Distortion Correction": "2D", + "Static Field Correction": "Off", + "Normalize": "Off" + }, + "Geometry - Common": { + "Slice Group": "1", + "Slices": "60", + "Distance Factor": "0 %", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "TR": "800.0 ms", + "Multi-Slice Mode": "Interleaved", + "Series": "Interleaved", + "Multi-band accel. factor": "6" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "L0.0 P8.0 H6.0", + "L": "0.0 mm", + "P": "8.0 mm", + "H": "6.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "Geometry - Saturation": { + "Special Saturation": "None" + }, + "Geometry - Tim Planning Suite": { + "Set-n-Go Protocol": "Off", + "Table Position": "6 mm", + "Table Position #2": "H", + "Inline Composing": "Off" + }, + "System - Miscellaneous": { + "Coil Selection": "Manual", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combination": "Sum of Squares", + "Matrix Optimization": "Off" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Standard", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off" + }, + "System - Adjust Volume": { + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "216 mm", + "R >> L": "216 mm", + "F >> H": "144 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm", + "Excitation": "Standard" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249549 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Correction Factor": "1.00", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "800.0 ms", + "Log Signals": "Off", + "Multi-band accel. factor": "6" + }, + "BOLD": { + "GLM Statistics": "Off", + "Ignore Meas. at Start": "0", + "Ignore After Transition": "0", + "Model Transition States": "On", + "Temp. Highpass Filter": "On", + "Threshold": "4.00", + "Paradigm Size": "3", + "Meas[1]": "Baseline", + "Meas[2]": "Baseline", + "Meas[3]": "Active", + "Motion Correction": "Off", + "Spatial Filter": "Off", + "Measurements": "383", + "Delay in TR": "0.00 ms" + }, + "Sequence - Part 1": { + "Sequence Name": "epfid", + "Dimension": "2D", + "Excitation": "Standard", + "Gradient Mode": "Performance", + "Flow Compensation": "None", + "Bandwidth": "2778 Hz/Px", + "Echo Spacing": "0.49 ms", + "Free Echo Spacing": "Off", + "EPI Factor": "90" + }, + "Sequence - Part 2": { + "Introduction": "Off", + "RF Spoiling": "Off" + }, + "Sequence - Special": { + "Excite pulse duration": "5960 us", + "Min. prep scans": "0", + "Min. prep scans SB": "0", + "Delay before PC scans": "0 us", + "Single-band images": "On", + "MB LeakBlock kernel": "On", + "MB dual kernel": "Off", + "MB RF phase scramble": "Off", + "Opt. MB RF pulse BW": "Off", + "SENSE1 coil combine": "Off", + "Invert RO/PE polarity": "On", + "Disable freq. update": "Off", + "Suppress 16-bit DICOM": "Off", + "Force equal slice timing": "Off", + "Online multi-band recon.": "Online", + "FFT scale factor": "1.00", + "Physio recording": "Off", + "Triggering scheme": "Standard" + }, + "Sequence - Assistant": { + "SAR Assistant": "Off" + } + }, + "pages": [ + 38, + 39 + ] + }, + { + "index": 16, + "name": "ABCD_fMRI_rest_MGH", + "path": "\\\\Research\\Investigators\\Frederick\\Potpourri_P1_changed\\ABCD_fMRI_rest_MGH", + "header": { + "ta": "5:14 min", + "coil_selection": "Auto", + "voxel_size_mm": "2.4×2.4×2.4", + "pat": "12", + "rel_snr": "1.00", + "sequence": "epfid" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'epfid' is a Siemens kernel", + "prints 10 sequence-specific parameter(s) no signature accounts for, including ACS mode, CC Mode, FLEET Dummy Pulses" + ], + "special_parameters": 10 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "Off", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Slice Group": "1", + "Slices": "60", + "Distance Factor": "0 %", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "TR": "800.0 ms", + "TE": "30.00 ms", + "Averages": "1", + "Concatenations": "1", + "AutoAlign": "---" + }, + "Contrast - Common": { + "TR": "800.0 ms", + "TE": "30.00 ms", + "MTC": "Off", + "Flip Angle": "90 deg", + "Fat-Water Contrast": "Fat Saturation", + "Reconstruction": "Magnitude" + }, + "Contrast - Dynamic": { + "Dynamic Mode": "Standard", + "Measurements": "383", + "Delay in TR": "0.00 ms" + }, + "Resolution - Common": { + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "Base Resolution": "90", + "Phase Resolution": "100 %", + "Interpolation": "Off" + }, + "Resolution - Acceleration": { + "Acceleration Mode": "SMS", + "Reference Scans": "EPI/Separate", + "Acceleration Factor PE": "2", + "Reference Lines PE": "44", + "SMS Factor": "6", + "FOV Shift Factor": "2", + "Phase Partial Fourier": "Off" + }, + "Resolution - Filter": { + "Raw Filter": "Off", + "Elliptical Filter": "Off", + "Hamming": "Off", + "Distortion Correction": "2D", + "Static Field Correction": "Off", + "Normalize": "Off" + }, + "Geometry - Common": { + "Slice Group": "1", + "Slices": "60", + "Distance Factor": "0 %", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "216 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "2.4 mm", + "TR": "800.0 ms", + "Multi-Slice Mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "L0.0 P8.0 H6.0", + "L": "0.0 mm", + "P": "8.0 mm", + "H": "6.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "Geometry - Saturation": { + "Special Saturation": "None" + }, + "Geometry - Tim Planning Suite": { + "Set-n-Go Protocol": "Off", + "Table Position": "6 mm", + "Table Position #2": "H", + "Inline Composing": "Off" + }, + "System - Miscellaneous": { + "Coil Selection": "Auto Coil Select", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combination": "Sum of Squares", + "Matrix Optimization": "Off", + "Coil Focus": "Flat" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Standard", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off" + }, + "System - Adjust Volume": { + "Position": "L0.0 P8.0 H6.0 mm", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "216 mm", + "R >> L": "216 mm", + "F >> H": "144 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm", + "Excitation": "Standard" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249549 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "800.0 ms", + "Log Signals": "Off", + "Concatenations": "1" + }, + "BOLD": { + "GLM Statistics": "Off", + "Ignore Meas. at Start": "0", + "Ignore After Transition": "0", + "Model Transition States": "On", + "Temp. Highpass Filter": "On", + "Threshold": "4.00", + "Paradigm Size": "20", + "Meas[1]": "Baseline", + "Meas[2]": "Baseline", + "Meas[3]": "Baseline", + "Meas[4]": "Baseline", + "Meas[5]": "Baseline", + "Meas[6]": "Baseline", + "Meas[7]": "Baseline", + "Meas[8]": "Baseline", + "Meas[9]": "Baseline", + "Meas[10]": "Baseline", + "Meas[11]": "Active", + "Meas[12]": "Active", + "Meas[13]": "Active", + "Meas[14]": "Active", + "Meas[15]": "Active", + "Meas[16]": "Active", + "Meas[17]": "Active", + "Meas[18]": "Active", + "Meas[19]": "Active", + "Meas[20]": "Active", + "Motion Correction": "Off", + "Spatial Filter": "Off", + "Measurements": "383", + "Delay in TR": "0.00 ms" + }, + "Sequence - Part 1": { + "Sequence Name": "epfid", + "Excitation": "Standard", + "RF Pulse Type": "Normal", + "Gradient Mode": "Performance", + "Bandwidth": "2778 Hz/Px", + "Echo Spacing": "0.49 ms", + "Free Echo Spacing": "Off", + "EPI Factor": "90" + }, + "Sequence - Part 2": { + "Introduction": "Off" + }, + "Sequence - Special": { + "Imaging Dummy TRs": "0", + "SMS ACS Dummy TRs": "-1", + "FLEET Dummy Pulses": "0", + "CC Mode": "Direct adj coil", + "RF Clip": "0", + "VERSE Factor": "1.00", + "ACS mode": "Standard", + "Kernel Size": "3x3", + "Wait for TCP/IP Trigger": "Off", + "Reverse Phase Encoding": "On" + }, + "Sequence - Assistant": { + "SAR Assistant": "Off" + } + }, + "pages": [ + 40, + 41, + 42 + ] + }, + { + "index": 17, + "name": "can_neuromelanin", + "path": "\\\\Research\\Investigators\\Frederick\\Potpourri_P1_changed\\can_neuromelanin", + "header": { + "ta": "14 sec", + "coil_selection": "Auto", + "voxel_size_mm": "2.3×2.3×5.0", + "pat": "None", + "rel_snr": "1.00", + "sequence": "fl" + }, + "provenance": { + "verdict": "unrecognized", + "evidence": [ + "sequence binary 'fl' is a Siemens kernel", + "prints 2 sequence-specific parameter(s) no signature accounts for, including MT Flip Angle, MT Offset" + ], + "special_parameters": 2 + }, + "sections": { + "Properties": { + "Start measurement without further preparation": "On", + "Wait for User to Start": "Off", + "Start measurements": "Single Measurement", + "Prio Recon": "Off", + "Auto Open Inline Display": "Off", + "Auto Close Inline Display": "Off", + "Load Images to MR View&GO": "On", + "Auto Store Images": "On", + "Disable auto transfer to PACS": "Off", + "Load Images to Stamp Segments": "Off", + "Load Images to Graphic Segments": "Off", + "Graphic segment": "Default", + "Inline Movie": "Off" + }, + "Routine": { + "Slice Group": "1", + "Slices": "1", + "Distance Factor": "20 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "5.0 mm", + "TR": "100.0 ms", + "TE": "10.00 ms", + "Averages": "1", + "Concatenations": "1", + "AutoAlign": "---" + }, + "Contrast - Common": { + "TR": "100.0 ms", + "TE": "10.00 ms", + "MTC": "Off", + "Magn. Preparation": "None", + "Flip Angle": "25 deg", + "Fat-Water Contrast": "Standard", + "Dark Blood": "Off", + "Contrasts": "1", + "SWI": "Off", + "Reconstruction": "Magnitude" + }, + "Contrast - Dynamic": { + "Dynamic Mode": "Standard", + "Measurements": "1", + "Multiple Series": "Each Measurement" + }, + "Resolution - Common": { + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "5.0 mm", + "Base Resolution": "128", + "Phase Resolution": "100 %", + "Interpolation": "Off" + }, + "Resolution - Acceleration": { + "Acceleration Mode": "None", + "Phase Partial Fourier": "Off", + "Asymmetric Echo": "Off" + }, + "Resolution - Filter": { + "Raw Filter": "Off", + "Elliptical Filter": "Off", + "Distortion Correction": "2D", + "Normalize": "Off", + "Image Filter": "Off" + }, + "Geometry - Common": { + "Slice Group": "1", + "Slices": "1", + "Distance Factor": "20 %", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "Phase Oversampling": "0 %", + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Slice Thickness": "5.0 mm", + "TR": "100.0 ms", + "Multi-Slice Mode": "Interleaved", + "Series": "Interleaved", + "Concatenations": "1" + }, + "Geometry - AutoAlign": { + "Slice Group": "1", + "Position": "Isocenter", + "Orientation": "Transversal", + "Phase Encoding Dir.": "A >> P", + "AutoAlign": "---", + "Initial Position": "Isocenter", + "L": "0.0 mm", + "P": "0.0 mm", + "H": "0.0 mm", + "Initial Orientation": "Transversal", + "Initial Rotation": "0.00 deg" + }, + "Geometry - Saturation": { + "Saturation Mode": "Standard", + "Special Saturation": "None" + }, + "Geometry - Tim Planning Suite": { + "Set-n-Go Protocol": "Off", + "Table Position": "0 mm", + "Table Position #2": "H", + "Inline Composing": "Off" + }, + "System - Miscellaneous": { + "Coil Selection": "Auto Coil Select", + "Radial Sorting": "Off", + "MSMA": "S - C - T", + "Sagittal": "R >> L", + "Coronal": "A >> P", + "Transversal": "F >> H", + "Coil Combination": "Adaptive Combine", + "Matrix Optimization": "Off", + "Coil Focus": "Flat" + }, + "System - Adjustments": { + "Adjustment Strategy": "Standard", + "B0 Shim": "Tune up", + "B1 Shim": "TrueForm", + "Adjustment Tolerance": "Auto", + "Adjust with Body Coil": "Off", + "Confirm Frequency": "Never", + "Assume Silicone": "Off" + }, + "System - Adjust Volume": { + "Position": "Isocenter", + "Orientation": "Transversal", + "Rotation": "0.00 deg", + "A >> P": "263 mm", + "R >> L": "350 mm", + "F >> H": "350 mm", + "Reset": "Off" + }, + "System - pTx": { + "B1 Shim": "TrueForm", + "Excitation": "Slice-sel.", + "LR Balancing": "Off" + }, + "System - Tx/Rx": { + "Frequency 1H": "123.249549 MHz", + "? Ref. Amplitude 1H": "0.000 V", + "Reset": "Off", + "Image Scaling": "1.000" + }, + "Physio - Signal": { + "1st Signal/Mode": "None", + "TR": "100.0 ms", + "Segments": "1", + "Concatenations": "1" + }, + "Physio - Cardiac": { + "Fat-Water Contrast": "Standard", + "Magn. Preparation": "None", + "Dark Blood": "Off", + "FOV Read": "300 mm", + "FOV Phase": "100.0 %", + "Phase Resolution": "100 %" + }, + "Physio - PACE": { + "Resp. Control": "Off", + "Concatenations": "1" + }, + "Inline - Liver": { + "Liver Registration": "Off", + "Save Original Images": "On" + }, + "Inline - Subtraction": { + "Subtract": "Off", + "Measurements": "1", + "StdDev": "Off", + "Save Original Images": "On" + }, + "Inline - MIP": { + "MIP Sag": "Off", + "MIP Cor": "Off", + "MIP Tra": "Off", + "MIP Time": "Off", + "Radial MIP": "Off", + "Save Original Images": "On", + "MPR Sag": "Off", + "MPR Cor": "Off", + "MPR Tra": "Off" + }, + "Inline - Soft Tissue": { + "Wash-in": "Off", + "Wash-out": "Off", + "TTP": "Off", + "PEI": "Off", + "MIP Time": "Off", + "Measurements": "1" + }, + "Inline - Composing": { + "Inline Composing": "Off" + }, + "Sequence - Part 1": { + "Sequence Name": "fl", + "Dimension": "2D", + "Excitation": "Slice-sel.", + "RF Pulse Type": "Normal", + "Gradient Mode": "Fast", + "Flow Compensation": "None", + "Bandwidth": "260 Hz/Px", + "Asymmetric Echo": "Off", + "Segments": "1" + }, + "Sequence - Part 2": { + "Introduction": "On", + "RF Spoiling": "On", + "Acoustic noise reduction": "Off" + }, + "Sequence - Special": { + "MT Flip Angle": "360 degrees", + "MT Offset": "1490 Hz" + }, + "Sequence - Assistant": { + "SAR Assistant": "Off", + "Allowed Delay": "0 s" + } + }, + "pages": [ + 43, + 44, + 45 + ] + } + ] +} diff --git a/tests/golden/XA60-Potpourri.json b/tests/golden/XA60-Potpourri_P2.json similarity index 99% rename from tests/golden/XA60-Potpourri.json rename to tests/golden/XA60-Potpourri_P2.json index 541861a..97ed573 100644 --- a/tests/golden/XA60-Potpourri.json +++ b/tests/golden/XA60-Potpourri_P2.json @@ -1,5 +1,5 @@ { - "source_file": "examples/XA60/Potpourri.pdf", + "source_file": "examples/XA60/Potpourri_P2.pdf", "software_version": "XA60", "detection": { "method": "header-string", diff --git a/tests/test_exar.py b/tests/test_exar.py index d4929f9..e77c403 100644 --- a/tests/test_exar.py +++ b/tests/test_exar.py @@ -15,7 +15,12 @@ import pytest -from conftest import archive_path, find_exar, requires_exar # noqa: F401 (fixture) +from conftest import ( # noqa: F401 (fixtures) + archive_path, + find_exar, + protocol_archive_path, + requires_exar, +) from siemens_protocol import exar from siemens_protocol.exar import archive, envelope, store from siemens_protocol.pipeline import parse_document @@ -205,7 +210,7 @@ def test_unpacking_no_children_yields_no_ids() -> None: @requires_exar -def test_the_archive_reads_at_a_real_branch_head(archive_path: str) -> None: +def test_the_archive_reads_at_a_real_branch_head(protocol_archive_path: str) -> None: """The placeholder branch is never chosen, and the head has live instances. Every archive carries a second branch whose baseline is ``-`` and which @@ -214,14 +219,14 @@ def test_the_archive_reads_at_a_real_branch_head(archive_path: str) -> None: Parameters ---------- - archive_path : str + protocol_archive_path : str Archive under test. Returns ------- None """ - loaded = exar.read(archive_path) + loaded = exar.read(protocol_archive_path) assert loaded.baseline != archive.PLACEHOLDER_BASELINE assert loaded.major_version.startswith("VA") assert loaded.instances @@ -229,7 +234,7 @@ def test_the_archive_reads_at_a_real_branch_head(archive_path: str) -> None: @requires_exar -def test_step_order_is_the_link_chain_not_the_children_blob(archive_path: str) -> None: +def test_step_order_is_the_link_chain_not_the_children_blob(protocol_archive_path: str) -> None: """Running order comes from the program's linked list. The program's ``Children`` blob holds the same steps in a different order. @@ -239,14 +244,14 @@ def test_step_order_is_the_link_chain_not_the_children_blob(archive_path: str) - Parameters ---------- - archive_path : str + protocol_archive_path : str Archive under test. Returns ------- None """ - loaded = exar.read(archive_path) + loaded = exar.read(protocol_archive_path) program = loaded.program assert program is not None chain = loaded.step_order() @@ -260,19 +265,19 @@ def test_step_order_is_the_link_chain_not_the_children_blob(archive_path: str) - @requires_exar -def test_every_step_is_named_and_holds_a_protocol(archive_path: str) -> None: +def test_every_step_is_named_and_holds_a_protocol(protocol_archive_path: str) -> None: """Names resolve through the label element, and each step runs a protocol. Parameters ---------- - archive_path : str + protocol_archive_path : str Archive under test. Returns ------- None """ - steps = exar.read(archive_path).steps + steps = exar.read(protocol_archive_path).steps assert steps for step in steps: assert step.name, f"step {step.instance.object_id} has no name" @@ -454,7 +459,7 @@ def test_the_archive_scan_list_matches_its_pdf_export() -> None: ------- None """ - archive_file = find_exar("Potpourri.exar1") + archive_file = find_exar("Potpourri_P2.exar1") pdf = os.path.splitext(archive_file)[0] + ".pdf" if not os.path.isfile(pdf): pytest.skip(f"no PDF export beside {os.path.basename(archive_file)}") diff --git a/tests/test_exar_patch.py b/tests/test_exar_patch.py index 60faf13..4c49e1e 100644 --- a/tests/test_exar_patch.py +++ b/tests/test_exar_patch.py @@ -16,11 +16,20 @@ from __future__ import annotations +import json import pathlib +import re +import subprocess +import sys import pytest -from conftest import find_exar, requires_exar +from conftest import ( # noqa: F401 + find_exar, + find_pdf, + protocol_archive_path, + requires_exar, +) from siemens_protocol.exar import patch, read #: The parameter the reference pair records a controlled edit for. @@ -73,8 +82,8 @@ def test_patching_reproduces_the_console_edit(tmp_path: pathlib.Path) -> None: ------- None """ - source = find_exar("Potpourri.exar1") - target = find_exar("Potpourri_changed.exar1") + source = find_exar("Potpourri_P2.exar1") + target = find_exar("Potpourri_P2_changed.exar1") wanted = _changed_steps(source, target) assert wanted, "the reference pair records no TR change to reproduce" @@ -98,6 +107,207 @@ def test_patching_reproduces_the_console_edit(tmp_path: pathlib.Path) -> None: ), f"ASCCONV alTR[0] differs on {one.name}" +@requires_exar +def test_patching_reproduces_the_multi_parameter_console_edit(tmp_path: pathlib.Path) -> None: + """The P1 pair is an answer key for every mapping at once. + + Potpourri_P1_changed is the same export re-saved after changing many + parameters across five scans, Special card included. Asking the patcher for + exactly those values and comparing every mapped assignment -- at every + array index -- exercises scope, arrays, units, the derived basis, re-hashing + and the container rewiring together. + + FOV Phase is compared to within the console's own rounding rather than + exactly: it is quantised to a ratio the hardware can realise and printed to + a tenth of a percent, so a percentage cannot reconstruct the millimetres it + came from. Everything else must match byte for byte. + + Parameters + ---------- + tmp_path : pathlib.Path + Destination for the patched archive. + + Returns + ------- + None + """ + source = find_exar("Potpourri_P1.exar1") + target = find_exar("Potpourri_P1_changed.exar1") + before, after = read(source), read(target) + + wanted: dict[str, dict[str, object]] = {} + for one, other in zip(before.steps, after.steps): + asked: dict[str, object] = {} + for mapping in patch.MAPPINGS: + if not patch.applies_to(mapping, one.protocol): + continue + if mapping.preview_path is not None: + was = one.protocol.preview.get(mapping.preview_path) + now = other.protocol.preview.get(mapping.preview_path) + if was is not None and now is not None and was.value != now.value: + asked[mapping.label] = now.value + continue + was_raw = patch.read_ascconv(one.protocol.xprotocol, mapping.ascconv_key) + now_raw = patch.read_ascconv(other.protocol.xprotocol, mapping.ascconv_key) + if mapping.bit is not None: + was_on = bool(int(was_raw or 0) >> mapping.bit & 1) + now_on = bool(int(now_raw or 0) >> mapping.bit & 1) + if was_on != now_on: + asked[mapping.label] = now_on + continue + if was_raw is not None and now_raw is not None and was_raw != now_raw: + asked[mapping.label] = float(now_raw) + if asked: + wanted[one.name] = asked + assert wanted, "the reference pair records no mapped change to reproduce" + + archive = read(source) + manifest = patch.apply(archive, wanted) + assert manifest.complete, manifest.report() + written = tmp_path / "patched.exar1" + archive.write(str(written)) + + ours = read(str(written)) + exact = approximate = 0 + for one, other in zip(ours.steps, after.steps): + for mapping in patch.MAPPINGS: + if not patch.applies_to(mapping, other.protocol): + continue + for key, _index in patch.expand(mapping.ascconv_key, other.protocol.xprotocol): + got = patch.read_ascconv(one.protocol.xprotocol, key) + want = patch.read_ascconv(other.protocol.xprotocol, key) + if got is None or want is None: + continue + if mapping.bit is not None: + # Compare the bit this mapping claims, not the whole word. + # The console also sets flags no shipped mapping covers -- + # this export toggled "Echoes in separate series", which no + # option scan has pinned -- and those share the word. + mine = int(got) >> mapping.bit & 1 + theirs = int(want) >> mapping.bit & 1 + assert mine == theirs, f"{one.name} {key} bit {mapping.bit}" + exact += 1 + continue + if got == want: + exact += 1 + continue + assert mapping.basis is not None, f"{one.name} {key}: {got} != {want}" + assert abs(float(got) - float(want)) <= 5e-4 * max(1.0, abs(float(want))) + approximate += 1 + assert exact > 1000, f"only {exact} assignments compared" + assert approximate, "the quantised parameter was not exercised" + + +#: Archives whose scans are one sequence repeated with a single Special-card +#: option changed each time. They are what pins the WIP indices, the enum +#: values and the flag bits, none of which can be read off a single export. +OPTION_SCANS = ( + "CMRR_optionscan_P1", + "MEMPRAGE_optionscan_P1", + "NAV_optionscan_P1", +) + +#: Units the card prints beside a value and the protocol does not store. +UNIT_SUFFIX = re.compile(r"\s*(ms|TRs|deg|Hz|%)$") + + +def _printed(scan: dict) -> dict[str, object]: + """Flatten one parsed scan to ``{parameter: printed value}``. + + Parameters + ---------- + scan : dict + One entry of a parsed protocol's ``scans``. + + Returns + ------- + dict + Every parameter the scan prints, keyed by name. + """ + return { + key: (item.get("value") if isinstance(item, dict) else item) + for key, item in (scan.get("flat") or {}).items() + } + + +@requires_exar +@pytest.mark.parametrize("name", OPTION_SCANS) +def test_replaying_every_single_option_toggle_matches_the_console(name: str) -> None: + """Each option scan is dozens of one-change answer keys in one file. + + Every scan after the first in a sequence group differs from the group's + baseline by one Special-card option, so asking the patcher for that one + label and comparing what it wrote against what the console wrote tests the + index, the encoding and the sparse-array behaviour at once. A flag is + compared at its own bit rather than by the whole word, since the console + also sets flags no shipped mapping covers and they share that word. + + Parameters + ---------- + name : str + Base name of the option-scan pair. + + Returns + ------- + None + """ + archive = read(find_exar(f"{name}.exar1")) + printed = json.loads( + subprocess.run( + [ + sys.executable, + "-m", + "siemens_protocol.cli", + "parse", + find_pdf(f"{name}.pdf"), + "--stdout", + ], + capture_output=True, + text=True, + check=True, + ).stdout + )["scans"] + assert len(printed) == len(archive.steps) + + groups: dict[str, list[int]] = {} + for position, step in enumerate(archive.steps): + groups.setdefault(patch.sequence_of(step.protocol), []).append(position) + + replayed = 0 + for positions in groups.values(): + first = positions[0] + baseline = archive.steps[first].protocol + was = _printed(printed[first]) + for position in positions[1:]: + now = _printed(printed[position]) + asked = {} + for label, value in now.items(): + if was.get(label) == value: + continue + mapping, _reason = patch.resolve(baseline, label) + if mapping is not None: + asked[label] = UNIT_SUFFIX.sub("", str(value)).strip() + if not asked: + continue + replayed += 1 + document, _applied, skipped = patch.patch_document(baseline, asked) + assert not skipped, [s.reason for s in skipped] + target = archive.steps[position].protocol.xprotocol + for label in asked: + mapping, _reason = patch.resolve(baseline, label) + assert mapping is not None + for key, _index in patch.expand(mapping.ascconv_key, target): + ours = patch.read_ascconv(document["Data"], key) + theirs = patch.read_ascconv(target, key) + if mapping.bit is not None: + assert (int(ours or 0) >> mapping.bit & 1) == ( + int(theirs or 0) >> mapping.bit & 1 + ), f"scan {position}: {label} at {key} bit {mapping.bit}" + else: + assert ours == theirs, f"scan {position}: {label} at {key}" + assert replayed >= 5, f"{name} exercised only {replayed} toggles" + + @requires_exar def test_a_patch_writes_both_locations_not_just_the_preview() -> None: """The preview and the ASCCONV block move together. @@ -109,7 +319,7 @@ def test_a_patch_writes_both_locations_not_just_the_preview() -> None: ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) step = archive.steps[0] before = patch.read_ascconv(step.protocol.xprotocol, "alTR[0]") document, applied, skipped = patch.patch_document(step.protocol, {"TR": 1234.0}) @@ -132,7 +342,7 @@ def test_the_millisecond_to_microsecond_scale_is_applied() -> None: ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) document, applied, _ = patch.patch_document(archive.steps[0].protocol, {"TR": 2000.0}) assert applied[0].value == 2000.0 assert patch.read_ascconv(document["Data"], "alTR[0]") == "2000000" @@ -201,16 +411,16 @@ def test_an_assignment_outside_the_ascconv_block_is_left_alone() -> None: def test_an_unmapped_label_is_reported_not_written() -> None: """A parameter the PDF prints but no mapping covers is skipped by name. - ``FOV Read`` is the live example: two ASCCONV keys hold the same number - throughout the corpus, so no mapping ships and the request must surface - rather than pick one. + ``Bandwidth`` is the live example: the PDF prints it on every scan and no + controlled edit has pinned where it is stored, so the request must surface + rather than be guessed at. Returns ------- None """ - archive = read(find_exar("Potpourri.exar1")) - _, applied, skipped = patch.patch_document(archive.steps[0].protocol, {"FOV Read": 210.0}) + archive = read(find_exar("Potpourri_P2.exar1")) + _, applied, skipped = patch.patch_document(archive.steps[0].protocol, {"Bandwidth": 2000.0}) assert not applied assert len(skipped) == 1 assert ( @@ -227,7 +437,7 @@ def test_a_request_for_a_missing_step_is_skipped_with_a_reason() -> None: ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) manifest = patch.apply(archive, {"no_such_scan": {"TR": 100.0}}) assert not manifest.complete assert manifest.skipped[0].reason == "no such step in archive" @@ -241,7 +451,7 @@ def test_a_protocol_without_the_field_is_skipped_not_invented() -> None: ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) lacking = [s for s in archive.steps if "sub.0.msr.ips" not in s.protocol.preview] if not lacking: pytest.skip("every protocol in this archive carries sub.0.msr.ips") @@ -271,7 +481,7 @@ def test_a_patch_re_addresses_only_the_protocol_it_touched(tmp_path: pathlib.Pat ------- None """ - path = find_exar("Potpourri.exar1") + path = find_exar("Potpourri_P2.exar1") archive = read(path) name = archive.steps[0].name before = {s.name: s.protocol.instance.content_hash for s in archive.steps} @@ -292,7 +502,7 @@ def test_a_run_that_writes_nothing_leaves_the_archive_alone(tmp_path: pathlib.Pa ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) before = {s.name: s.protocol.instance.content_hash for s in archive.steps} manifest = patch.apply(archive, {archive.steps[0].name: {"Nonexistent Parameter": 1}}) assert not manifest.applied @@ -313,7 +523,7 @@ def test_the_patched_archive_survives_a_write_and_read(tmp_path: pathlib.Path) - ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) name = archive.steps[3].name patch.apply(archive, {name: {"TR": 1750.0}}) written = tmp_path / "patched.exar1" @@ -343,7 +553,7 @@ def test_the_manifest_counts_what_it_did_not_write() -> None: ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) name = archive.steps[0].name manifest = patch.apply(archive, {name: {"TR": 900.0}}) assert manifest.inherited > 0 @@ -358,7 +568,7 @@ def test_the_manifest_names_the_values_the_console_would_recompute() -> None: ------- None """ - archive = read(find_exar("Potpourri.exar1")) + archive = read(find_exar("Potpourri_P2.exar1")) manifest = patch.apply(archive, {archive.steps[0].name: {"TR": 900.0}}) assert "lScanTimeSec" in manifest.stale assert "not recomputed" in manifest.report() @@ -370,38 +580,161 @@ def test_the_manifest_names_the_values_the_console_would_recompute() -> None: @requires_exar -def test_every_shipped_mapping_agrees_with_the_corpus(archive_path: str) -> None: - """Each mapping's two locations hold the same value in every protocol. +def test_every_shipped_mapping_agrees_with_the_corpus(protocol_archive_path: str) -> None: + """Each mapping's stored value matches its displayed one, in every protocol. - This is the evidence the table rests on, re-checked rather than trusted: - a mapping whose scale or key is wrong shows up as a disagreement here. + This re-derives the evidence the table rests on rather than trusting it: a + wrong scale, key or basis shows up as a disagreement. Array targets are + checked at every index, not just the first, since a mapping that wrote one + slice and left the rest is exactly the bug this catches. Parameters ---------- - archive_path : str - One archive from the corpus. + protocol_archive_path : str + One archive from the corpus that carries protocols. Returns ------- None """ - archive = read(archive_path) + archive = read(protocol_archive_path) checked = 0 for step in archive.steps: protocol = step.protocol - for mapping in patch.MAPPINGS.values(): + for mapping in patch.MAPPINGS: + if mapping.preview_path is None or not patch.applies_to(mapping, protocol): + continue entry = protocol.preview.get(mapping.preview_path) - literal = patch.read_ascconv(protocol.xprotocol, mapping.ascconv_key) - if entry is None or literal is None or not isinstance(entry.value, (int, float)): + if entry is None or not isinstance(entry.value, (int, float)): continue - checked += 1 - assert float(literal) == pytest.approx(entry.value * mapping.scale), ( - f"{step.name}: {mapping.label} preview {entry.value} does not match " - f"{mapping.ascconv_key}={literal} at scale {mapping.scale}" - ) + for key, index in patch.expand(mapping.ascconv_key, protocol.xprotocol): + literal = patch.read_ascconv(protocol.xprotocol, key) + if literal is None: + continue + want = float(entry.value) * mapping.scale + if mapping.basis is not None: + basis = patch.read_ascconv( + protocol.xprotocol, mapping.basis.replace("[*]", f"[{index}]") + ) + if basis is None: + continue + want *= float(basis) + checked += 1 + # FOV Phase is quantised by the console and printed rounded to a + # tenth of a percent, so it agrees to within that rounding and + # not exactly. Everything else is exact. + tolerance = 2e-3 if mapping.basis is not None else 1e-6 + assert abs(float(literal) - want) <= tolerance * max(1.0, abs(want)), ( + f"{step.name}: {mapping.label} shows {entry.value} but " + f"{key}={literal}, wanted {want}" + ) assert checked, "no mapping was exercised by this archive" +@requires_exar +def test_a_sequence_specific_mapping_is_refused_on_another_sequence() -> None: + """``sWipMemBlock`` indices mean different things per sequence. + + ``alFree[0]`` is MT Flip Angle on ``can_neuromelanin`` and a packed word of + checkbox flags on CMRR's multiband sequences, so a table that wrote it + without regard to the sequence would put a flip angle into CMRR's flags. + + Returns + ------- + None + """ + archive = read(find_exar("Potpourri_P1.exar1")) + steps = {s.name: s for s in archive.steps} + cmrr = steps["Minn_CMRR_2.3mm_S8_rest_6min"].protocol + neuro = steps["can_neuromelanin"].protocol + assert patch.sequence_of(cmrr) == "cmrr_mbep2d_bold" + assert patch.sequence_of(neuro) == "can_neuromelanin" + + found, _ = patch.resolve(neuro, "MT Flip Angle") + assert found is not None and found.ascconv_key == "sWipMemBlock.alFree[0]" + + refused, reason = patch.resolve(cmrr, "MT Flip Angle") + assert refused is None + assert "cmrr_mbep2d_bold" in reason + + +@requires_exar +def test_an_array_target_writes_every_slice_not_only_the_first() -> None: + """FOV Read and Slice Thickness are replicated across the slice array. + + Writing element zero alone leaves the others at the old value, which loads, + lists correctly in the console, and is wrong. + + Returns + ------- + None + """ + archive = read(find_exar("Potpourri_P1.exar1")) + step = {s.name: s for s in archive.steps}["Minn_CMRR_2.3mm_S8_rest_6min"] + targets = patch.expand("sSliceArray.asSlice[*].dReadoutFOV", step.protocol.xprotocol) + assert len(targets) > 1, "this fixture should have a multi-slice array" + + document, applied, skipped = patch.patch_document(step.protocol, {"FOV Read": 199.0}) + assert not skipped and len(applied) == 1 + written = {patch.read_ascconv(document["Data"], key) for key, _ in targets} + assert written == {"199.0"}, f"not every slice was written: {sorted(written)}" + + +@requires_exar +def test_a_derived_target_is_scaled_by_its_basis() -> None: + """FOV Phase is stored as millimetres, not as the percentage displayed. + + Returns + ------- + None + """ + archive = read(find_exar("Potpourri_P1.exar1")) + step = {s.name: s for s in archive.steps}["Minn_CMRR_2.3mm_S8_rest_6min"] + document, applied, skipped = patch.patch_document( + step.protocol, {"FOV Read": 200.0, "FOV Phase": 50.0} + ) + assert not skipped and len(applied) == 2 + assert patch.read_ascconv(document["Data"], "sSliceArray.asSlice[0].dReadoutFOV") == "200.0" + assert patch.read_ascconv(document["Data"], "sSliceArray.asSlice[0].dPhaseFOV") == "100.0" + + +@requires_exar +def test_a_special_card_mapping_writes_ascconv_with_no_preview_side() -> None: + """Nothing on the Special card appears in ``Preview``. + + The console lists only common parameters, so these mappings have no preview + entry to keep in sync and must not invent one. + + Returns + ------- + None + """ + archive = read(find_exar("Potpourri_P1.exar1")) + step = {s.name: s for s in archive.steps}["can_neuromelanin"] + assert not step.protocol.by_label("MT Flip Angle") + + before = dict(step.protocol.document["Preview"]) + document, applied, skipped = patch.patch_document(step.protocol, {"MT Flip Angle": 355}) + assert not skipped and len(applied) == 1 + assert patch.read_ascconv(document["Data"], "sWipMemBlock.alFree[0]") == "355" + assert document["Preview"] == before, "an ASCCONV-only mapping touched the preview" + + +def test_a_float_is_written_the_way_the_console_writes_one() -> None: + """Doubles carry twelve significant figures, not Python's full repr. + + A freshly computed value otherwise arrives with its binary tail attached -- + ``201.26200000000003`` where the console would write ``201.262``. + + Returns + ------- + None + """ + assert patch.format_like(201.26200000000003, "207.0") == "201.262" + assert patch.format_like(1.0, "2.0") == "1.0" + assert patch.format_like(2000000.0, "650000") == "2000000" + + def test_every_mapping_records_how_it_was_established() -> None: """No mapping ships without stating its evidence. @@ -413,18 +746,85 @@ def test_every_mapping_records_how_it_was_established() -> None: ------- None """ - for path, mapping in patch.MAPPINGS.items(): - assert mapping.preview_path == path + for mapping in patch.MAPPINGS: assert mapping.evidence.strip() assert mapping.scale > 0 + assert mapping.label.strip() + # sWipMemBlock is scratch memory with no global meaning, so anything + # reaching into it must say which sequences it is true of. + if "sWipMemBlock" in mapping.ascconv_key: + assert mapping.is_sequence_specific, f"{mapping.label} must name its sequences" def test_no_two_mappings_claim_the_same_ascconv_key() -> None: - """Two preview paths writing one assignment would race each other. + """Distinct entries are distinguished by more than their target. + + Two mappings may share a key when their conditions are disjoint -- slice + thickness writes ``dThickness`` on both 2D and 3D acquisitions, meaning + different things -- so the identity of an entry is the target together with + the scope it applies in. Returns ------- None """ - keys = [m.ascconv_key for m in patch.MAPPINGS.values()] - assert len(keys) == len(set(keys)) + identity = [(m.ascconv_key, m.sequences, m.when, m.bit) for m in patch.MAPPINGS] + assert len(identity) == len(set(identity)) + + +@requires_exar +def test_no_protocol_has_two_mappings_writing_one_key(protocol_archive_path: str) -> None: + """The safety property the entry-level check only approximates. + + Sharing a key is fine while the conditions are disjoint, and fine for + checkboxes packed into one word -- fourteen CMRR options live in + ``alFree[0]`` and touch a bit each. What would race is two mappings in + scope for one protocol writing the same *whole* assignment. + + Parameters + ---------- + protocol_archive_path : str + One archive from the corpus that carries protocols. + + Returns + ------- + None + """ + archive = read(protocol_archive_path) + for step in archive.steps: + protocol = step.protocol + keys = [(m.ascconv_key, m.bit) for m in patch.MAPPINGS if patch.applies_to(m, protocol)] + assert len(keys) == len(set(keys)), ( + f"{step.name} ({patch.sequence_of(protocol)}) has two mappings " + f"writing one key: {sorted(k for k in keys if keys.count(k) > 1)}" + ) + + +@requires_exar +def test_slice_thickness_follows_the_acquisition_dimension() -> None: + """On a 3D acquisition ``dThickness`` is the slab, not the slice. + + Writing the displayed thickness straight into it would put 1.0 where the + protocol holds 176.0 -- a protocol that loads and is badly wrong. + + Returns + ------- + None + """ + archive = read(find_exar("Potpourri_P1.exar1")) + steps = {s.name: s for s in archive.steps} + flat = steps["Minn_CMRR_2.3mm_S8_rest_6min"].protocol + slab = steps["ABCD_T1w_MPR_vNav"].protocol + assert patch.read_ascconv(flat.xprotocol, "sKSpace.ucDimension") == "2" + assert patch.read_ascconv(slab.xprotocol, "sKSpace.ucDimension") == "4" + + two_d, _ = patch.resolve(flat, "Slice Thickness") + three_d, _ = patch.resolve(slab, "Slice Thickness") + assert two_d is not None and two_d.basis is None + assert three_d is not None and three_d.basis == "sKSpace.lImagesPerSlab" + + partitions = float(patch.read_ascconv(slab.xprotocol, "sKSpace.lImagesPerSlab")) + document, applied, skipped = patch.patch_document(slab, {"Slice Thickness": 1.25}) + assert not skipped and len(applied) == 1 + written = float(patch.read_ascconv(document["Data"], "sSliceArray.asSlice[0].dThickness")) + assert written == 1.25 * partitions diff --git a/tests/test_scans.py b/tests/test_scans.py index 1954536..116beb8 100644 --- a/tests/test_scans.py +++ b/tests/test_scans.py @@ -54,11 +54,26 @@ "XA60/NSSI_ROUTINE.pdf": 12, "VE11C/Healthy Control NSSI HOOD.pdf": 18, "XA60/Healthy Control NSSI HOOD.pdf": 18, - # Potpourri ships beside its own .exar1 export, so this count is not - # eyeballed off the printout: it is the number of measurement steps in - # the archive's program chain, reached by a route that shares no code - # with the PDF splitter. tests/test_exar.py asserts the names match too. - "Potpourri.pdf": 18, + # Potpourri ships beside its own .exar1 export, so these counts are not + # eyeballed off the printout: 18 is the number of measurement steps in the + # archive's program chain, reached by a route that shares no code with the + # PDF splitter. tests/test_exar.py asserts the names match too. P1 and P2 + # are the same protocol imported onto two XA60 scanners and agree, which + # is a third independent check on the same number. + # The three option scans hold one sequence repeated with a single Special + # card option changed each time; their counts are the number of steps in + # each archive's program chain, so they are cross-checked the same way + # Potpourri is. The two VE11C spectroscopy protocols have no archive and + # are checked against their own contents pages instead. + "XA60/CMRR_optionscan_P1.pdf": 33, + "XA60/MEMPRAGE_optionscan_P1.pdf": 7, + "XA60/NAV_optionscan_P1.pdf": 31, + "VE11C/31P CSI 20230503 NOE.pdf": 13, + "XA60/31P CSI 20230503 NOE.pdf": 13, + "VE11C/BEEST_SPICE_11112025.pdf": 24, + "Potpourri_P1.pdf": 18, + "Potpourri_P1_changed.pdf": 18, + "Potpourri_P2.pdf": 18, "ELS2_20210802XA60.pdf": 15, "NOCICEPT_Ph2MRI515_SecondXA60.pdf": 19, # XA30 counts are cross-checked against each export's table of contents, diff --git a/tests/test_sequences.py b/tests/test_sequences.py index b1482f8..e0df81b 100644 --- a/tests/test_sequences.py +++ b/tests/test_sequences.py @@ -677,14 +677,44 @@ def test_the_stated_owner_never_contradicts_the_other_detectors() -> None: #: signatures for them would mean attributing sequences from inference alone, #: which the catalog's rule against guessed attributions forbids -- and #: 'unrecognized' is the honest verdict for a scan a person should look at. -UNACCOUNTED = { - ("XA60-Potpourri.json", "ep2d_bold_mgh"), - ("XA60-Potpourri.json", "ep2d_diff_mgh"), - ("XA60-Potpourri.json", "ep2d_se_sms_mgh"), - ("XA60-Potpourri.json", "ABCD_fMRI_rest_MGH"), - ("XA60-Potpourri.json", "can_neuromelanin"), +#: The five scans, and the three exports of the one protocol that prints them. +#: Potpourri now ships as P1 and P2 -- the same protocol imported onto two XA60 +#: scanners -- plus P1_changed, so the same five recur in each. Kept as a +#: product of two small sets rather than fifteen literals, because the fact +#: being pinned is "these five scans, in every Potpourri export" and a flat +#: list would obscure a case where one export gained a sixth. +UNACCOUNTED_SCANS = { + "ep2d_bold_mgh", + "ep2d_diff_mgh", + "ep2d_se_sms_mgh", + "ABCD_fMRI_rest_MGH", + "can_neuromelanin", +} +UNACCOUNTED_EXPORTS = { + "XA60-Potpourri_P1.json", + "XA60-Potpourri_P1_changed.json", + "XA60-Potpourri_P2.json", +} + +#: Spectroscopy scans that no signature accounts for, in two VE11C protocols +#: added for their own sake rather than for sequence detection. ``head_csi_fid`` +#: and ``SPECIAL_ACC`` are spectroscopy kernels, and ``can_neuromelanin`` here +#: is the VE11C build of a sequence the XA60 examples also print. Naming them +#: is the honest record: writing signatures would mean attributing sequences +#: from inference, which the catalog's rules forbid. +UNACCOUNTED_ELSEWHERE = { + ("VE11C-31P CSI 20230503 NOE.json", "SPECIAL_ACC"), + ("VE11C-31P CSI 20230503 NOE.json", "head_csi_fid"), + ("VE11C-BEEST_SPICE_11112025.json", "can_neuromelanin"), + # The same 31P protocol exported from XA60. Its SPECIAL_ACC scan resolves + # there and does not on VE11C, so the two exports differ by one entry. + ("XA60-31P CSI 20230503 NOE.json", "head_csi_fid"), } +UNACCOUNTED = { + (export, scan) for export in UNACCOUNTED_EXPORTS for scan in UNACCOUNTED_SCANS +} | UNACCOUNTED_ELSEWHERE + @requires_snapshots def test_the_shipped_examples_are_accounted_for_apart_from_a_pinned_few() -> None: