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RF: Write out anatomical template derivatives #3136

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merged 4 commits into from
Nov 19, 2023
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RF: Write out anatomical template derivatives #3136

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f0eff51
ENH: Add volumetric and CIFTI anatomical outputs
effigies Nov 19, 2023
691dd54
RF: Reuse cortical mask ROI and downsampled midthickness
effigies Nov 19, 2023
92ded31
FIX: Ensure BOLD is not oversampled for anat
effigies Nov 19, 2023
2319fef
CI: Update expected outputs [no fasttrack]
effigies Nov 19, 2023
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22 changes: 22 additions & 0 deletions .circleci/ds005_partial_fasttrack_outputs.txt
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Expand Up @@ -22,6 +22,28 @@ sub-01/anat/sub-01_hemi-R_desc-preproc_white.surf.gii
sub-01/anat/sub-01_hemi-R_desc-reg_sphere.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_space-fsLR_den-91k_desc-preproc_curv.dscalar.nii
sub-01/anat/sub-01_space-fsLR_den-91k_desc-preproc_curv.json
sub-01/anat/sub-01_space-fsLR_den-91k_desc-preproc_sulc.dscalar.nii
sub-01/anat/sub-01_space-fsLR_den-91k_desc-preproc_sulc.json
sub-01/anat/sub-01_space-fsLR_den-91k_desc-preproc_thickness.dscalar.nii
sub-01/anat/sub-01_space-fsLR_den-91k_desc-preproc_thickness.json
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_dseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_desc-preproc_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-GM_desc-preproc_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-WM_desc-preproc_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.json
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_dseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.json
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_desc-preproc_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_desc-preproc_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_desc-preproc_probseg.nii.gz
sub-01/fmap
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
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22 changes: 22 additions & 0 deletions .circleci/ds005_partial_outputs.txt
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Expand Up @@ -44,6 +44,28 @@ sub-01/anat/sub-01_hemi-R_white.surf.gii
sub-01/anat/sub-01_label-CSF_probseg.nii.gz
sub-01/anat/sub-01_label-GM_probseg.nii.gz
sub-01/anat/sub-01_label-WM_probseg.nii.gz
sub-01/anat/sub-01_space-fsLR_den-91k_curv.dscalar.nii
sub-01/anat/sub-01_space-fsLR_den-91k_curv.json
sub-01/anat/sub-01_space-fsLR_den-91k_sulc.dscalar.nii
sub-01/anat/sub-01_space-fsLR_den-91k_sulc.json
sub-01/anat/sub-01_space-fsLR_den-91k_thickness.dscalar.nii
sub-01/anat/sub-01_space-fsLR_den-91k_thickness.json
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.json
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.json
sub-01/anat/sub-01_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_dseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
sub-01/fmap
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
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10 changes: 10 additions & 0 deletions .circleci/ds054_fasttrack_outputs.txt
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Expand Up @@ -7,6 +7,16 @@ logs/CITATION.html
logs/CITATION.md
logs/CITATION.tex
sub-100185
sub-100185/anat
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-preproc_dseg.json
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-preproc_dseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.json
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-CSF_desc-preproc_probseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-GM_desc-preproc_probseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-WM_desc-preproc_probseg.nii.gz
sub-100185/fmap
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
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9 changes: 9 additions & 0 deletions .circleci/ds054_outputs.txt
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Expand Up @@ -18,6 +18,15 @@ sub-100185/anat/sub-100185_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
sub-100185/anat/sub-100185_label-CSF_probseg.nii.gz
sub-100185/anat/sub-100185_label-GM_probseg.nii.gz
sub-100185/anat/sub-100185_label-WM_probseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.json
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.json
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_dseg.json
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_dseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-CSF_probseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-GM_probseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-WM_probseg.nii.gz
sub-100185/fmap
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
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9 changes: 9 additions & 0 deletions .circleci/ds210_fasttrack_outputs.txt
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Expand Up @@ -7,6 +7,15 @@ logs/CITATION.html
logs/CITATION.md
logs/CITATION.tex
sub-02
sub-02/anat
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-preproc_dseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_desc-preproc_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_desc-preproc_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_desc-preproc_probseg.nii.gz
sub-02/fmap
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
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8 changes: 8 additions & 0 deletions .circleci/ds210_outputs.txt
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Expand Up @@ -18,6 +18,14 @@ sub-02/anat/sub-02_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
sub-02/anat/sub-02_label-CSF_probseg.nii.gz
sub-02/anat/sub-02_label-GM_probseg.nii.gz
sub-02/anat/sub-02_label-WM_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_dseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
sub-02/fmap
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
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122 changes: 114 additions & 8 deletions fmriprep/workflows/base.py
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Expand Up @@ -152,7 +152,18 @@
from niworkflows.utils.misc import fix_multi_T1w_source_name
from niworkflows.utils.spaces import Reference
from smriprep.workflows.anatomical import init_anat_fit_wf
from smriprep.workflows.outputs import init_template_iterator_wf
from smriprep.workflows.outputs import (

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init_ds_anat_volumes_wf,
init_ds_grayord_metrics_wf,
init_ds_surface_metrics_wf,
init_template_iterator_wf,
)
from smriprep.workflows.surfaces import (

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init_gifti_morphometrics_wf,
init_hcp_morphometrics_wf,
init_morph_grayords_wf,
init_resample_midthickness_wf,
)

from fmriprep.workflows.bold.base import init_bold_wf

Expand Down Expand Up @@ -302,10 +313,14 @@
run_without_submitting=True,
)

bids_root = str(config.execution.bids_dir)
fmriprep_dir = str(config.execution.fmriprep_dir)
omp_nthreads = config.nipype.omp_nthreads

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# Build the workflow
anat_fit_wf = init_anat_fit_wf(
bids_root=str(config.execution.bids_dir),
output_dir=str(config.execution.fmriprep_dir),
bids_root=bids_root,
output_dir=fmriprep_dir,
freesurfer=config.workflow.run_reconall,
hires=config.workflow.hires,
longitudinal=config.workflow.longitudinal,
Expand All @@ -316,7 +331,7 @@
skull_strip_template=Reference.from_string(config.workflow.skull_strip_template)[0],
spaces=spaces,
precomputed=anatomical_cache,
omp_nthreads=config.nipype.omp_nthreads,
omp_nthreads=omp_nthreads,
sloppy=config.execution.sloppy,
skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
)
Expand Down Expand Up @@ -347,11 +362,30 @@
if config.workflow.level == "full":
if spaces.cached.get_spaces(nonstandard=False, dim=(3,)):
template_iterator_wf = init_template_iterator_wf(spaces=spaces)
ds_std_volumes_wf = init_ds_anat_volumes_wf(

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bids_root=bids_root,
output_dir=fmriprep_dir,
name="ds_std_volumes_wf",
)
workflow.connect([
(anat_fit_wf, template_iterator_wf, [
('outputnode.template', 'inputnode.template'),
('outputnode.anat2std_xfm', 'inputnode.anat2std_xfm'),
]),
(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"),
]),
(template_iterator_wf, ds_std_volumes_wf, [
("outputnode.std_t1w", "inputnode.ref_file"),
("outputnode.anat2std_xfm", "inputnode.anat2std_xfm"),
("outputnode.space", "inputnode.space"),
("outputnode.cohort", "inputnode.cohort"),
("outputnode.resolution", "inputnode.resolution"),
]),
]) # fmt:skip

if 'MNI152NLin2009cAsym' in spaces.get_spaces():
Expand Down Expand Up @@ -395,6 +429,73 @@
]),
]) # fmt:skip

# Create CIFTI morphometrics
curv_wf = init_gifti_morphometrics_wf(morphometrics=['curv'], name='curv_wf')
hcp_morphometrics_wf = init_hcp_morphometrics_wf(omp_nthreads=omp_nthreads)
morph_grayords_wf = init_morph_grayords_wf(

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grayord_density=config.workflow.cifti_output,
omp_nthreads=omp_nthreads,
)
resample_midthickness_wf = init_resample_midthickness_wf(

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grayord_density=config.workflow.cifti_output,
)
ds_grayord_metrics_wf = init_ds_grayord_metrics_wf(

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bids_root=bids_root,
output_dir=fmriprep_dir,
metrics=["curv", "thickness", "sulc"],
cifti_output=config.workflow.cifti_output,
)

workflow.connect([

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(anat_fit_wf, curv_wf, [
("outputnode.subject_id", "inputnode.subject_id"),
("outputnode.subjects_dir", "inputnode.subjects_dir"),
]),
(anat_fit_wf, hcp_morphometrics_wf, [
("outputnode.subject_id", "inputnode.subject_id"),
("outputnode.thickness", "inputnode.thickness"),
("outputnode.sulc", "inputnode.sulc"),
("outputnode.midthickness", "inputnode.midthickness"),
]),
(curv_wf, hcp_morphometrics_wf, [
("outputnode.curv", "inputnode.curv"),
]),
(anat_fit_wf, resample_midthickness_wf, [
('outputnode.midthickness', 'inputnode.midthickness'),
(
f"outputnode.sphere_reg_{'msm' if msm_sulc else 'fsLR'}",
"inputnode.sphere_reg_fsLR",
),
]),
(anat_fit_wf, morph_grayords_wf, [
("outputnode.midthickness", "inputnode.midthickness"),
(
f'outputnode.sphere_reg_{"msm" if msm_sulc else "fsLR"}',
'inputnode.sphere_reg_fsLR',
),
]),
(hcp_morphometrics_wf, morph_grayords_wf, [
("outputnode.curv", "inputnode.curv"),
("outputnode.thickness", "inputnode.thickness"),
("outputnode.sulc", "inputnode.sulc"),
("outputnode.roi", "inputnode.roi"),
]),
(resample_midthickness_wf, morph_grayords_wf, [
('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
]),
(anat_fit_wf, ds_grayord_metrics_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"),
("outputnode.thickness_fsLR", "inputnode.thickness"),
("outputnode.thickness_metadata", "inputnode.thickness_metadata"),
("outputnode.sulc_fsLR", "inputnode.sulc"),
("outputnode.sulc_metadata", "inputnode.sulc_metadata"),
]),
]) # fmt:skip

if config.workflow.anat_only:
return clean_datasinks(workflow)

Expand All @@ -421,8 +522,8 @@
fmap_wf = init_fmap_preproc_wf(
debug="fieldmaps" in config.execution.debug,
estimators=fmap_estimators,
omp_nthreads=config.nipype.omp_nthreads,
output_dir=str(config.execution.fmriprep_dir),
omp_nthreads=omp_nthreads,
output_dir=fmriprep_dir,
subject=subject_id,
)
fmap_wf.__desc__ = f"""
Expand Down Expand Up @@ -481,7 +582,7 @@
s.metadata for s in estimator.sources if s.suffix in ("bold", "sbref")
]
syn_preprocessing_wf = init_syn_preprocessing_wf(
omp_nthreads=config.nipype.omp_nthreads,
omp_nthreads=omp_nthreads,
debug=config.execution.sloppy,
auto_bold_nss=True,
t1w_inversion=False,
Expand Down Expand Up @@ -561,7 +662,6 @@
('outputnode.white', 'inputnode.white'),
('outputnode.pial', 'inputnode.pial'),
('outputnode.midthickness', 'inputnode.midthickness'),
('outputnode.thickness', 'inputnode.thickness'),
('outputnode.anat_ribbon', 'inputnode.anat_ribbon'),
(
f'outputnode.sphere_reg_{"msm" if msm_sulc else "fsLR"}',
Expand Down Expand Up @@ -609,6 +709,12 @@
workflow.connect([
(select_MNI6_xfm, bold_wf, [("anat2std_xfm", "inputnode.anat2mni6_xfm")]),
(select_MNI6_tpl, bold_wf, [("brain_mask", "inputnode.mni6_mask")]),
(hcp_morphometrics_wf, bold_wf, [
("outputnode.roi", "inputnode.cortex_mask"),
]),
(resample_midthickness_wf, bold_wf, [
('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
]),
]) # fmt:skip

return clean_datasinks(workflow)
Expand Down
9 changes: 5 additions & 4 deletions fmriprep/workflows/bold/base.py
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Expand Up @@ -113,8 +113,6 @@
FreeSurfer pial surfaces, in T1w space, collated left, then right
sphere_reg_fsLR
Registration spheres from fsnative to fsLR space, collated left, then right
thickness
FreeSurfer thickness metrics, collated left, then right
anat_ribbon
Binary cortical ribbon mask in T1w space
fmap_id
Expand Down Expand Up @@ -235,7 +233,8 @@
"midthickness",
"pial",
"sphere_reg_fsLR",
"thickness",
"midthickness_fsLR",
"cortex_mask",
"anat_ribbon",
# Fieldmap registration
"fmap",
Expand Down Expand Up @@ -316,6 +315,7 @@
omp_nthreads=omp_nthreads,
name='bold_anat_wf',
)
bold_anat_wf.inputs.inputnode.resolution = "native"

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fmriprep/workflows/bold/base.py#L318 

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workflow.connect([
(inputnode, bold_native_wf, [
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("white", "inputnode.white"),
("pial", "inputnode.pial"),
("midthickness", "inputnode.midthickness"),
("thickness", "inputnode.thickness"),
("midthickness_fsLR", "inputnode.midthickness_fsLR"),
("sphere_reg_fsLR", "inputnode.sphere_reg_fsLR"),
("cortex_mask", "inputnode.cortex_mask"),
("anat_ribbon", "inputnode.anat_ribbon"),
]),
(bold_anat_wf, bold_fsLR_resampling_wf, [
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