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FIX: Use t1w2fsnative_xfm to resample segmentations #201

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merged 3 commits into from
Jun 7, 2020
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FIX: Use t1w2fsnative_xfm to resample segmentations #201

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b56c615
FIX: Use fsnative2t1w_xfm to resample segmentations
effigies Jun 7, 2020
e7ac6da
docs: Fix intersphinx's link to NiWorkflows after migration to NiPreps
oesteban Feb 29, 2020
7933c1b
CI: Upgrade pip<21 before upgrading setuptools for Py2
effigies Jun 7, 2020
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3 changes: 2 additions & 1 deletion .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -247,7 +247,8 @@ jobs:
pyenv local $PY2
echo -n "Python version: "
python --version
pip install --upgrade pip setuptools
pip install --upgrade "pip<21"
pip install --upgrade setuptools
pip install --upgrade wrapper/
which smriprep-docker
smriprep-docker -i poldracklab/smriprep:latest --help
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2 changes: 1 addition & 1 deletion docs/conf.py
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Expand Up @@ -232,7 +232,7 @@
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
'python': ('https://docs.python.org/', None),
'niworkflows': ('https://poldracklab.github.io/niworkflows/', None),
'niworkflows': ('https://www.nipreps.org/niworkflows/', None),
}

# -- Options for versioning extension ----------------------------------------
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24 changes: 14 additions & 10 deletions smriprep/workflows/surfaces.py
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Expand Up @@ -231,10 +231,12 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
(autorecon_resume_wf, aseg_to_native_wf, [
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id')]),
(fsnative2t1w_xfm, aseg_to_native_wf, [('out_reg_file', 'inputnode.fsnative2t1w_xfm')]),
(inputnode, aparc_to_native_wf, [('corrected_t1', 'inputnode.in_file')]),
(autorecon_resume_wf, aparc_to_native_wf, [
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id')]),
(fsnative2t1w_xfm, aparc_to_native_wf, [('out_reg_file', 'inputnode.fsnative2t1w_xfm')]),
(aseg_to_native_wf, refine, [('outputnode.out_file', 'in_aseg')]),

# Output
Expand Down Expand Up @@ -502,6 +504,8 @@ def init_segs_to_native_wf(name='segs_to_native', segmentation='aseg'):
FreeSurfer SUBJECTS_DIR
subject_id
FreeSurfer subject ID
fsnative2t1w_xfm
LTA-style affine matrix translating from FreeSurfer-conformed subject space to T1w

Outputs
-------
Expand All @@ -510,13 +514,15 @@ def init_segs_to_native_wf(name='segs_to_native', segmentation='aseg'):

"""
workflow = Workflow(name='%s_%s' % (name, segmentation))
inputnode = pe.Node(niu.IdentityInterface([
'in_file', 'subjects_dir', 'subject_id']), name='inputnode')
inputnode = pe.Node(
niu.IdentityInterface(['in_file', 'subjects_dir', 'subject_id', 'fsnative2t1w_xfm']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(['out_file']), name='outputnode')
# Extract the aseg and aparc+aseg outputs
fssource = pe.Node(nio.FreeSurferSource(), name='fs_datasource')
tonative = pe.Node(fs.Label2Vol(), name='tonative')
tonii = pe.Node(fs.MRIConvert(out_type='niigz', resample_type='nearest'), name='tonii')
# Resample from T1.mgz to T1w.nii.gz, applying any offset in fsnative2t1w_xfm,
# and convert to NIfTI while we're at it
resample = pe.Node(fs.ApplyVolTransform(transformed_file='seg.nii.gz'), name='resample')

if segmentation.startswith('aparc'):
if segmentation == 'aparc_aseg':
Expand All @@ -531,12 +537,10 @@ def _sel(x): return [parc for parc in x if 'DKTatlas+' in parc][0] # noqa
(inputnode, fssource, [
('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id')]),
(inputnode, tonii, [('in_file', 'reslice_like')]),
(fssource, tonative, [(segmentation, 'seg_file'),
('rawavg', 'template_file'),
('aseg', 'reg_header')]),
(tonative, tonii, [('vol_label_file', 'in_file')]),
(tonii, outputnode, [('out_file', 'out_file')]),
(inputnode, resample, [('in_file', 'target_file'),
('fsnative2t1w_xfm', 'lta_file')]),
(fssource, resample, [(segmentation, 'source_file')]),
(resample, outputnode, [('transformed_file', 'out_file')]),
])
return workflow

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