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♻️ Refactor niworkflow-ants for skullstripping #1403

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♻️ Refactor niworkflow-ants for skullstripping #1403

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b666677
:recycle: Import and monkeypatch `niworkflows.anat.ants.init_brain_ex…
shnizzedy Nov 24, 2020
723bb77
:memo: Add flowchart and examples for niworkflows-ants
shnizzedy Nov 25, 2020
410226a
:recycle: Update workflow connections for refactored niworkflows-ants
shnizzedy Nov 25, 2020
9b2eca0
:arrow_up: Add script to install specific version of ANTs
shnizzedy Nov 25, 2020
9b539cc
:arrow_up: Upgrade ANTs to v2.3.4 (from 2.1.0)
shnizzedy Nov 25, 2020
fb72555
:construction_worker: Use conda to install cython
shnizzedy Nov 30, 2020
fc7a397
:arrow_up: Upgrade prov @ 1.5.2 (from 1.5.0)
shnizzedy Nov 30, 2020
3944cdd
:arrow_up: Upgrade nibable @ 3.0.1 (from 2.3.3)
shnizzedy Nov 30, 2020
4dee45b
:bug: Pass memory managment paramters to niworkflows-ants skullstripping
shnizzedy Dec 1, 2020
5a9db2b
:hammer: Simplify ANTs build script
shnizzedy Dec 1, 2020
0490512
:hammer: Fix `CMAKE_INSTALL_PREFIX`
shnizzedy Dec 1, 2020
1892add
:alembic: Replace 'MultiProc' with 'LegacyMultiProc'
shnizzedy Dec 3, 2020
d979ab3
:construction_worker: Authenticate to GitHub Container Registry
shnizzedy Dec 2, 2020
fdeff66
:construction: Make ANTS registration verbose (for debugging)
shnizzedy Dec 3, 2020
1e6fe2e
:package: Build from base image that already includes ANTS 2.3.4
shnizzedy Dec 3, 2020
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3 changes: 3 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -37,6 +37,9 @@ commands:
cd ..
build-images:
steps:
- run:
name: "Logging into GitHub Container Registry"
command: echo "${GITHUB_REGISTRY_TOKEN}" | docker login https://docker.pkg.github.com -u ${GITHUB_REGISTRY_NAME} --password-stdin
- run:
name: "Building Docker image"
command: |
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2 changes: 1 addition & 1 deletion CPAC/GUI/interface/windows/main_window.py
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Expand Up @@ -268,7 +268,7 @@ def runAnalysis1(self, pipeline, sublist, p):
pass

CPAC.pipeline.cpac_runner.run(sublist, pipeline, p,
plugin='MultiProc',
plugin='LegacyMultiProc',
plugin_args=plugin_args)

def runIndividualAnalysis(self, event):
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2 changes: 1 addition & 1 deletion CPAC/alff/alff.py
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Expand Up @@ -276,7 +276,7 @@ def run_alff(input_fmri, func_brain_mask, hp=0.01, lp=0.1, out_dir=None,

if run:
workflow.run(
plugin='MultiProc', plugin_args={'n_procs': num_cores_per_subject})
plugin='LegacyMultiProc', plugin_args={'n_procs': num_cores_per_subject})
outpath = glob.glob(os.path.join(workflow_dir, output, '*'))
return outpath

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17 changes: 11 additions & 6 deletions CPAC/anat_preproc/anat_preproc.py
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Expand Up @@ -377,18 +377,23 @@ def skullstrip_anatomical(method='afni', config=None, wf_name='skullstrip_anatom

elif method == 'niworkflows-ants':
# Skull-stripping using niworkflows-ants
anat_skullstrip_ants = init_brain_extraction_wf(tpl_target_path=config.niworkflows_ants_template_path,
tpl_mask_path=config.niworkflows_ants_mask_path,
tpl_regmask_path=config.niworkflows_ants_regmask_path,
name='anat_skullstrip_ants')
anat_skullstrip_ants = init_brain_extraction_wf(
tpl_target_path=config.niworkflows_ants_template_path,
tpl_mask_path=config.niworkflows_ants_mask_path,
tpl_regmask_path=config.niworkflows_ants_regmask_path,
name='anat_skullstrip_ants',
omp_nthreads=config.num_ants_threads,
mem_gb=(
config.maximumMemoryPerParticipant / config.num_ants_threads
))

preproc.connect(inputnode, 'anat_data',
anat_skullstrip_ants, 'inputnode.in_files')

preproc.connect(anat_skullstrip_ants, 'copy_xform.out_file',
preproc.connect(anat_skullstrip_ants, 'outputnode.out_file',
outputnode, 'skullstrip')

preproc.connect(anat_skullstrip_ants, 'copy_xform.out_file',
preproc.connect(anat_skullstrip_ants, 'outputnode.out_file',
outputnode, 'brain')

preproc.connect(anat_skullstrip_ants, 'atropos_wf.copy_xform.out_mask',
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