From 3f48d933ed7a956564a721701a1bda27d7e081c1 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Thu, 12 Dec 2024 11:36:42 -0500 Subject: [PATCH] Test collection on real data. --- .github/workflows/build-test-publish.yml | 5 +++++ sdcflows/utils/wrangler.py | 9 +++++++++ sdcflows/workflows/fit/medic.py | 8 +++++++- 3 files changed, 21 insertions(+), 1 deletion(-) diff --git a/.github/workflows/build-test-publish.yml b/.github/workflows/build-test-publish.yml index d3d5a03551..917d33c3b9 100644 --- a/.github/workflows/build-test-publish.yml +++ b/.github/workflows/build-test-publish.yml @@ -184,6 +184,11 @@ jobs: datalad update -r --merge -d hcph-pilot_fieldmaps/ datalad get -r -J 2 -d hcph-pilot_fieldmaps/ hcph-pilot_fieldmaps/* + # ds005250 + datalad install -r https://gin.g-node.org/tsalo/ds005250-sdcflows.git + datalad update -r --merge -d ds005250-sdcflows/ + datalad get -r -J 2 -d ds005250-sdcflows/ ds005250-sdcflows/sub-04/ses-2/ + - name: Set FreeSurfer variables run: | echo "FREESURFER_HOME=$HOME/.cache/freesurfer" >> $GITHUB_ENV diff --git a/sdcflows/utils/wrangler.py b/sdcflows/utils/wrangler.py index c5dbc0d61f..1576996181 100644 --- a/sdcflows/utils/wrangler.py +++ b/sdcflows/utils/wrangler.py @@ -321,6 +321,15 @@ def find_estimators( FieldmapEstimation(sources=<2 files>, method=, bids_id='auto_...')] + >>> find_estimators( + ... layout=layouts['ds005250-sdcflows'], + ... subject='04', + ... fmapless=False, + ... force_fmapless=False, + ... bids_filters={'session': '2'}, + ... ) # doctest: +ELLIPSIS + [FieldmapEstimation(sources=<10 files>, method=, + bids_id='auto_...')] """ from .misc import create_logger from bids.layout import Query diff --git a/sdcflows/workflows/fit/medic.py b/sdcflows/workflows/fit/medic.py index 64885a8394..343d282d30 100644 --- a/sdcflows/workflows/fit/medic.py +++ b/sdcflows/workflows/fit/medic.py @@ -70,11 +70,17 @@ def init_medic_wf(name="medic_wf"): ----- This workflow performs minimal preparation before running the MEDIC algorithm, as implemented in ``vandandrew/warpkit``. + + Any downstream processing piplines that use this workflow should include + the following references in their boilerplate BibTeX file: + + - medic: https://doi.org/10.1101/2023.11.28.568744 """ workflow = Workflow(name=name) workflow.__desc__ = """\ -A dynamic fieldmap was estimated from multi-echo EPI data using the MEDIC algorithm (@medic). +Volume-wise *B0* nonuniformity maps (or *fieldmaps*) were estimated from +complex-valued, multi-echo EPI data using the MEDIC algorithm (@medic). """ inputnode = pe.Node(niu.IdentityInterface(fields=INPUT_FIELDS), name="inputnode")