Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: Output fsLR meshes on subject surfaces #3411

Merged
merged 3 commits into from
Dec 17, 2024
Merged

feat: Output fsLR meshes on subject surfaces #3411

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
4994d14
feat: Output fsLR meshes on subject surfaces
effigies Dec 13, 2024
9556e11
chore(ci): Expect fsLR surface outputs
effigies Dec 13, 2024
ebf0f3d
build: Fetch T2w templates
effigies Dec 13, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions .circleci/ds005_partial_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,17 @@ sub-01/anat/sub-01_desc-ribbon_mask.json
sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
sub-01/anat/sub-01_hemi-L_desc-preproc_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_desc-preproc_white.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_midthickness.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_pial.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_white.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_desc-preproc_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_desc-preproc_white.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_midthickness.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_pial.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_white.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
Expand Down
6 changes: 6 additions & 0 deletions .circleci/ds005_partial_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,9 @@ sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
sub-01/anat/sub-01_hemi-L_pial.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_pial.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_white.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
Expand All @@ -34,6 +37,9 @@ sub-01/anat/sub-01_hemi-L_thickness.shape.gii
sub-01/anat/sub-01_hemi-L_white.surf.gii
sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
sub-01/anat/sub-01_hemi-R_pial.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_pial.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_white.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
sub-01/anat/sub-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
Expand Down
31 changes: 26 additions & 5 deletions fmriprep/workflows/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -156,13 +156,14 @@ def init_single_subject_wf(subject_id: str):
from smriprep.workflows.outputs import (
init_ds_anat_volumes_wf,
init_ds_grayord_metrics_wf,
init_ds_surfaces_wf,
init_template_iterator_wf,
)
from smriprep.workflows.surfaces import (
init_gifti_morphometrics_wf,
init_hcp_morphometrics_wf,
init_morph_grayords_wf,
init_resample_midthickness_wf,
init_resample_surfaces_wf,
)

from fmriprep.workflows.bold.base import init_bold_wf
Expand Down Expand Up @@ -449,7 +450,8 @@ def init_single_subject_wf(subject_id: str):
grayord_density=config.workflow.cifti_output,
omp_nthreads=omp_nthreads,
)
resample_midthickness_wf = init_resample_midthickness_wf(
resample_surfaces_wf = init_resample_surfaces_wf(
surfaces=['white', 'pial', 'midthickness'],
grayord_density=config.workflow.cifti_output,
)
ds_grayord_metrics_wf = init_ds_grayord_metrics_wf(
Expand All @@ -458,6 +460,15 @@ def init_single_subject_wf(subject_id: str):
metrics=['curv', 'thickness', 'sulc'],
cifti_output=config.workflow.cifti_output,
)
ds_fsLR_surfaces_wf = init_ds_surfaces_wf(
output_dir=fmriprep_dir,
surfaces=['white', 'pial', 'midthickness'],
entities={
'space': 'fsLR',
'density': '32k' if config.workflow.cifti_output == '91k' else '59k',
},
name='ds_fsLR_surfaces_wf',
)

workflow.connect([
(anat_fit_wf, curv_wf, [
Expand All @@ -473,7 +484,9 @@ def init_single_subject_wf(subject_id: str):
(curv_wf, hcp_morphometrics_wf, [
('outputnode.curv', 'inputnode.curv'),
]),
(anat_fit_wf, resample_midthickness_wf, [
(anat_fit_wf, resample_surfaces_wf, [
('outputnode.white', 'inputnode.white'),
('outputnode.pial', 'inputnode.pial'),
('outputnode.midthickness', 'inputnode.midthickness'),
(
f"outputnode.sphere_reg_{'msm' if msm_sulc else 'fsLR'}",
Expand All @@ -493,12 +506,15 @@ def init_single_subject_wf(subject_id: str):
('outputnode.sulc', 'inputnode.sulc'),
('outputnode.roi', 'inputnode.roi'),
]),
(resample_midthickness_wf, morph_grayords_wf, [
(resample_surfaces_wf, morph_grayords_wf, [
('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
]),
(anat_fit_wf, ds_grayord_metrics_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
]),
(anat_fit_wf, ds_fsLR_surfaces_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
]),
(morph_grayords_wf, ds_grayord_metrics_wf, [
('outputnode.curv_fsLR', 'inputnode.curv'),
('outputnode.curv_metadata', 'inputnode.curv_metadata'),
Expand All @@ -507,6 +523,11 @@ def init_single_subject_wf(subject_id: str):
('outputnode.sulc_fsLR', 'inputnode.sulc'),
('outputnode.sulc_metadata', 'inputnode.sulc_metadata'),
]),
(resample_surfaces_wf, ds_fsLR_surfaces_wf, [
('outputnode.white_fsLR', 'inputnode.white'),
('outputnode.pial_fsLR', 'inputnode.pial'),
('outputnode.midthickness_fsLR', 'inputnode.midthickness'),
]),
]) # fmt:skip

if config.workflow.anat_only:
Expand Down Expand Up @@ -740,7 +761,7 @@ def init_single_subject_wf(subject_id: str):
(hcp_morphometrics_wf, bold_wf, [
('outputnode.roi', 'inputnode.cortex_mask'),
]),
(resample_midthickness_wf, bold_wf, [
(resample_surfaces_wf, bold_wf, [
('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
]),
]) # fmt:skip
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ dependencies = [
"pybids >= 0.16",
"requests >= 2.27",
"sdcflows >= 2.10.0",
"smriprep >= 0.16.0",
"smriprep @ git+https://github.com/nipreps/smriprep.git",
"tedana >= 23.0.2",
"templateflow >= 24.2.2",
"transforms3d >= 0.4",
Expand Down
4 changes: 3 additions & 1 deletion scripts/fetch_templates.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,9 @@ def fetch_MNI2009():
Expected templates:

tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T2w.nii.gz
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T2w.nii.gz
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz
Expand All @@ -25,7 +27,7 @@ def fetch_MNI2009():
"""
template = 'MNI152NLin2009cAsym'

tf.get(template, resolution=(1, 2), desc=None, suffix='T1w')
tf.get(template, resolution=(1, 2), desc=None, suffix=['T1w', 'T2w'])
tf.get(template, resolution=(1, 2), desc='brain', suffix='mask')
tf.get(template, resolution=1, atlas=None, desc='carpet', suffix='dseg')
tf.get(template, resolution=2, desc='fMRIPrep', suffix='boldref')
Expand Down
Loading