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Merged
skaliy merged 1 commit into from
Nov 12, 2026
Merged

docs(vs-pacs): removed redcap description of nnu-net #98

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7 changes: 3 additions & 4 deletions research/vestibular_schwannoma/deployment/pacs/README.md
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ROR/PACS container that runs the five-fold DynUNet ensemble on a CE-T1w series. CPU only:
each of the five models runs in its own worker with three threads, so it needs at least 15
CPU threads. TTA is on by default and averages the original and one copy flipped
anterior-posterior and inferior-superior (`TTA_FLIP_AXES` in `parallel_inference.py`), as in
the nnU-Net container. For the general workflow see
anterior-posterior and inferior-superior (`TTA_FLIP_AXES` in `parallel_inference.py`). For the
general workflow see
[Research PACS deployment with ROR](../../../RESEARCH_PACS_DEPLOYMENT.md).

## Build a release
Expand Down Expand Up @@ -100,8 +100,7 @@ There is no direct uploader; the PACS imports the file.

`redcap_model_instances.json` gives each bundle hash a permanent block of 100 instances,
stored as the base (a multiple of 100). DynUNet `c5642793...` has 200. Instance 1 is the manual
mask; nnU-Net large still writes its largest region to 10, and block 100 is planned for it.
Older DynUNet results at 11 (and 2/3 before that) are no longer updated.
mask. Older DynUNet results at 11 (and 2/3 before that) are no longer updated.

- A rerun of the same bundle overwrites its instances. If it finds fewer regions, the higher
instances of the earlier run stay.
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6 changes: 3 additions & 3 deletions research/vestibular_schwannoma/deployment/pacs/parallel_inference.py
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# Batch tensors have shape [B, C, X, Y, Z] after RAS+ reordering, so spatial axes 2, 3 and 4
# are left-right, anterior-posterior and inferior-superior. TTA averages the original and one
# copy flipped anterior-posterior and inferior-superior together, the same flip as the nnU-Net
# container. On the 344 held-out cases this had as few or fewer false positives than the other
# 2-flip sets, and about the same as all 8 flips at a quarter of the cost.
# copy flipped anterior-posterior and inferior-superior together. On the 344 held-out cases
# this had as few or fewer false positives than the other 2-flip sets, and about the same as
# all 8 flips at a quarter of the cost.
TTA_FLIP_AXES = ((), (3, 4))
TTA_DESCRIPTION = "original + one flip along anterior-posterior and inferior-superior"

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