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RF: Remove much of the hardcoded T1w fields in favor of anat #433

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merged 20 commits into from
Jul 26, 2024
Merged

RF: Remove much of the hardcoded T1w fields in favor of anat #433

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ad72b45
RF: Extend template workflow for other anatomical image types
mgxd Mar 27, 2024
e6e3501
RF: More T1w -> anat substitutions
mgxd Apr 3, 2024
54fc2ff
RF: Make more functions anatagnostic
mgxd Apr 11, 2024
3889004
RF: More t1w->anat
mgxd Apr 11, 2024
ce09d87
RF: Generalize anatomical reference used in surface workflows
mgxd Apr 18, 2024
3701d43
RF: Alter io fields within fit workflow
mgxd Apr 18, 2024
4614c94
RF: anat_second_derivatives_wf -> ds_fs_segs_wf
mgxd Apr 22, 2024
277ad07
FIX: Remnants of second_derivatives_wf, remove unused input
mgxd Apr 25, 2024
17e873b
FIX: Remove unused parameter, add conditional for dhcpAsym
mgxd Apr 28, 2024
5c7f02b
RF: Diversify ds_anat_volumes_wf anatomical inputs
mgxd Apr 28, 2024
bbddb11
ENH: Allow inclusion of additional BIDS entities to outputs
mgxd May 1, 2024
0025971
FIX: ds_template_wf connections, parameter
mgxd Jul 25, 2024
45fd797
FIX: ds_dseg_wf connections
mgxd Jul 25, 2024
8d2322f
FIX: ds_tpms_wf connections
mgxd Jul 25, 2024
79f3b17
FIX: Drop removed parameter
mgxd Jul 25, 2024
a66b7af
FIX: Add potential mask typing
mgxd Jul 25, 2024
4b7e22f
FIX: ds_std_volumes_wf connections
mgxd Jul 25, 2024
b034778
FIX: Refinement connection
mgxd Jul 25, 2024
0e1b7cb
DOC: Modify function signature
mgxd Jul 25, 2024
4a8a782
ENH: Require specifying image type for various datasink workflows
mgxd Jul 26, 2024
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80 changes: 35 additions & 45 deletions smriprep/workflows/anatomical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,10 +61,10 @@
from .fit.registration import init_register_template_wf
from .outputs import (
init_anat_reports_wf,
init_anat_second_derivatives_wf,
init_ds_anat_volumes_wf,
init_ds_dseg_wf,
init_ds_fs_registration_wf,
init_ds_fs_segs_wf,
init_ds_grayord_metrics_wf,
init_ds_mask_wf,
init_ds_surface_metrics_wf,
Expand Down Expand Up @@ -287,7 +287,6 @@ def init_anat_preproc_wf(
ds_std_volumes_wf = init_ds_anat_volumes_wf(
bids_root=bids_root,
output_dir=output_dir,
name='ds_std_volumes_wf',
)

workflow.connect([
Expand Down Expand Up @@ -320,10 +319,10 @@ def init_anat_preproc_wf(
]),
(anat_fit_wf, ds_std_volumes_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
('outputnode.t1w_preproc', 'inputnode.t1w_preproc'),
('outputnode.t1w_mask', 'inputnode.t1w_mask'),
('outputnode.t1w_dseg', 'inputnode.t1w_dseg'),
('outputnode.t1w_tpms', 'inputnode.t1w_tpms'),
('outputnode.t1w_preproc', 'inputnode.anat_preproc'),
('outputnode.t1w_mask', 'inputnode.anat_mask'),
('outputnode.t1w_dseg', 'inputnode.anat_dseg'),
('outputnode.t1w_tpms', 'inputnode.anat_tpms'),
]),
(template_iterator_wf, ds_std_volumes_wf, [
('outputnode.std_t1w', 'inputnode.ref_file'),
Expand All @@ -335,17 +334,12 @@ def init_anat_preproc_wf(
]) # fmt:skip

if freesurfer:
anat_second_derivatives_wf = init_anat_second_derivatives_wf(
ds_fs_segs_wf = init_ds_fs_segs_wf(
bids_root=bids_root,
output_dir=output_dir,
cifti_output=cifti_output,
)
surface_derivatives_wf = init_surface_derivatives_wf(
cifti_output=cifti_output,
)
ds_surfaces_wf = init_ds_surfaces_wf(
bids_root=bids_root, output_dir=output_dir, surfaces=['inflated']
)
surface_derivatives_wf = init_surface_derivatives_wf()
ds_surfaces_wf = init_ds_surfaces_wf(output_dir=output_dir, surfaces=['inflated'])
ds_curv_wf = init_ds_surface_metrics_wf(
bids_root=bids_root, output_dir=output_dir, metrics=['curv'], name='ds_curv_wf'
)
Expand All @@ -355,7 +349,7 @@ def init_anat_preproc_wf(
('outputnode.t1w_preproc', 'inputnode.reference'),
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
]),
(anat_fit_wf, ds_surfaces_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
Expand All @@ -369,12 +363,12 @@ def init_anat_preproc_wf(
(surface_derivatives_wf, ds_curv_wf, [
('outputnode.curv', 'inputnode.curv'),
]),
(anat_fit_wf, anat_second_derivatives_wf, [
(anat_fit_wf, ds_fs_segs_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
]),
(surface_derivatives_wf, anat_second_derivatives_wf, [
('outputnode.out_aseg', 'inputnode.t1w_fs_aseg'),
('outputnode.out_aparc', 'inputnode.t1w_fs_aparc'),
(surface_derivatives_wf, ds_fs_segs_wf, [
('outputnode.out_aseg', 'inputnode.anat_fs_aseg'),
('outputnode.out_aparc', 'inputnode.anat_fs_aparc'),
]),
(surface_derivatives_wf, outputnode, [
('outputnode.out_aseg', 't1w_aseg'),
Expand Down Expand Up @@ -765,10 +759,10 @@ def init_anat_fit_wf(
longitudinal=longitudinal,
omp_nthreads=omp_nthreads,
num_files=num_t1w,
contrast='T1w',
image_type='T1w',
name='anat_template_wf',
)
ds_template_wf = init_ds_template_wf(output_dir=output_dir, num_t1w=num_t1w)
ds_template_wf = init_ds_template_wf(output_dir=output_dir, num_anat=num_t1w)

# fmt:off
workflow.connect([
Expand All @@ -781,11 +775,11 @@ def init_anat_fit_wf(
('outputnode.out_report', 'inputnode.t1w_conform_report'),
]),
(anat_template_wf, ds_template_wf, [
('outputnode.anat_realign_xfm', 'inputnode.t1w_ref_xfms'),
('outputnode.anat_realign_xfm', 'inputnode.anat_ref_xfms'),
]),
(sourcefile_buffer, ds_template_wf, [('source_files', 'inputnode.source_files')]),
(t1w_buffer, ds_template_wf, [('t1w_preproc', 'inputnode.t1w_preproc')]),
(ds_template_wf, outputnode, [('outputnode.t1w_preproc', 't1w_preproc')]),
(t1w_buffer, ds_template_wf, [('t1w_preproc', 'inputnode.anat_preproc')]),
(ds_template_wf, outputnode, [('outputnode.anat_preproc', 't1w_preproc')]),
])
# fmt:on
else:
Expand Down Expand Up @@ -954,16 +948,16 @@ def init_anat_fit_wf(
workflow.connect([
(fast, lut_t1w_dseg, [('partial_volume_map', 'in_dseg')]),
(sourcefile_buffer, ds_dseg_wf, [('source_files', 'inputnode.source_files')]),
(lut_t1w_dseg, ds_dseg_wf, [('out', 'inputnode.t1w_dseg')]),
(ds_dseg_wf, seg_buffer, [('outputnode.t1w_dseg', 't1w_dseg')]),
(lut_t1w_dseg, ds_dseg_wf, [('out', 'inputnode.anat_dseg')]),
(ds_dseg_wf, seg_buffer, [('outputnode.anat_dseg', 't1w_dseg')]),
])
if not have_tpms:
ds_tpms_wf = init_ds_tpms_wf(output_dir=output_dir)
workflow.connect([
(fast, fast2bids, [('partial_volume_files', 'inlist')]),
(sourcefile_buffer, ds_tpms_wf, [('source_files', 'inputnode.source_files')]),
(fast2bids, ds_tpms_wf, [('out', 'inputnode.t1w_tpms')]),
(ds_tpms_wf, seg_buffer, [('outputnode.t1w_tpms', 't1w_tpms')]),
(fast2bids, ds_tpms_wf, [('out', 'inputnode.anat_tpms')]),
(ds_tpms_wf, seg_buffer, [('outputnode.anat_tpms', 't1w_tpms')]),
])
# fmt:on
else:
Expand Down Expand Up @@ -1088,10 +1082,10 @@ def init_anat_fit_wf(
('source_files', 'inputnode.source_files'),
]),
(surface_recon_wf, ds_fs_registration_wf, [
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
]),
(ds_fs_registration_wf, outputnode, [
('outputnode.fsnative2t1w_xfm', 'fsnative2t1w_xfm'),
('outputnode.fsnative2anat_xfm', 'fsnative2t1w_xfm'),
]),
])
# fmt:on
Expand All @@ -1114,7 +1108,7 @@ def init_anat_fit_wf(
(surface_recon_wf, refinement_wf, [
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
]),
(t1w_buffer, refinement_wf, [
('t1w_preproc', 'inputnode.reference_image'),
Expand All @@ -1135,7 +1129,7 @@ def init_anat_fit_wf(
longitudinal=longitudinal,
omp_nthreads=omp_nthreads,
num_files=len(t2w),
contrast='T2w',
image_type='T2w',
name='t2w_template_wf',
)
bbreg = pe.Node(
Expand Down Expand Up @@ -1216,15 +1210,13 @@ def init_anat_fit_wf(
LOGGER.info(f'ANAT Stage 8: Creating GIFTI surfaces for {surfs + spheres}')
if surfs:
gifti_surfaces_wf = init_gifti_surfaces_wf(surfaces=surfs)
ds_surfaces_wf = init_ds_surfaces_wf(
bids_root=bids_root, output_dir=output_dir, surfaces=surfs
)
ds_surfaces_wf = init_ds_surfaces_wf(output_dir=output_dir, surfaces=surfs)
# fmt:off
workflow.connect([
(surface_recon_wf, gifti_surfaces_wf, [
('outputnode.subject_id', 'inputnode.subject_id'),
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
]),
(gifti_surfaces_wf, surfaces_buffer, [
(f'outputnode.{surf}', surf) for surf in surfs
Expand All @@ -1240,7 +1232,7 @@ def init_anat_fit_wf(
surfaces=spheres, to_scanner=False, name='gifti_spheres_wf'
)
ds_spheres_wf = init_ds_surfaces_wf(
bids_root=bids_root, output_dir=output_dir, surfaces=spheres, name='ds_spheres_wf'
output_dir=output_dir, surfaces=spheres, name='ds_spheres_wf'
)
# fmt:off
workflow.connect([
Expand Down Expand Up @@ -1316,7 +1308,6 @@ def init_anat_fit_wf(
LOGGER.info('ANAT Stage 9: Creating fsLR registration sphere')
fsLR_reg_wf = init_fsLR_reg_wf()
ds_fsLR_reg_wf = init_ds_surfaces_wf(
bids_root=bids_root,
output_dir=output_dir,
surfaces=['sphere_reg_fsLR'],
name='ds_fsLR_reg_wf',
Expand All @@ -1341,7 +1332,6 @@ def init_anat_fit_wf(
LOGGER.info('ANAT Stage 10: Creating MSM-Sulc registration sphere')
msm_sulc_wf = init_msm_sulc_wf(sloppy=sloppy)
ds_msmsulc_wf = init_ds_surfaces_wf(
bids_root=bids_root,
output_dir=output_dir,
surfaces=['sphere_reg_msm'],
name='ds_msmsulc_wf',
Expand Down Expand Up @@ -1375,7 +1365,7 @@ def init_anat_template_wf(
longitudinal: bool,
omp_nthreads: int,
num_files: int,
contrast: str,
image_type: ty.Literal['T1w', 'T2w'] = 'T1w',
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name: str = 'anat_template_wf',
):
"""
Expand All @@ -1388,7 +1378,7 @@ def init_anat_template_wf(

from smriprep.workflows.anatomical import init_anat_template_wf
wf = init_anat_template_wf(
longitudinal=False, omp_nthreads=1, num_files=1, contrast="T1w"
longitudinal=False, omp_nthreads=1, num_files=1, image_type="T1w"
)

Parameters
Expand All @@ -1400,8 +1390,8 @@ def init_anat_template_wf(
Maximum number of threads an individual process may use
num_files : :obj:`int`
Number of images
contrast : :obj:`str`
Name of contrast, for reporting purposes, e.g., T1w, T2w, PDw
image_type : :obj:`str`
MR image type (T1w, T2w, etc.)
name : :obj:`str`, optional
Workflow name (default: anat_template_wf)

Expand All @@ -1427,8 +1417,8 @@ def init_anat_template_wf(
if num_files > 1:
fs_ver = fs.Info().looseversion() or '(version unknown)'
workflow.__desc__ = f"""\
An anatomical {contrast}-reference map was computed after registration of
{num_files} {contrast} images (after INU-correction) using
An anatomical {image_type}-reference map was computed after registration of
{num_files} {image} images (after INU-correction) using
`mri_robust_template` [FreeSurfer {fs_ver}, @fs_template].
"""

Expand Down
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