RF: Write out anatomical template derivatives

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -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

.circleci/ds005_partial_outputs.txt

@@ -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

.circleci/ds054_fasttrack_outputs.txt

@@ -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

.circleci/ds054_outputs.txt

@@ -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

.circleci/ds210_fasttrack_outputs.txt

@@ -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

.circleci/ds210_outputs.txt

@@ -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

fmriprep/workflows/base.py

@@ -152,7 +152,18 @@ def init_single_subject_wf(subject_id: str):
     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 (
+        init_ds_anat_volumes_wf,
+        init_ds_grayord_metrics_wf,
+        init_ds_surface_metrics_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,
+    )
 
     from fmriprep.workflows.bold.base import init_bold_wf
 
@@ -302,10 +313,14 @@ def init_single_subject_wf(subject_id: str):
         run_without_submitting=True,
     )
 
+    bids_root = str(config.execution.bids_dir)
+    fmriprep_dir = str(config.execution.fmriprep_dir)
+    omp_nthreads = config.nipype.omp_nthreads
+
     # 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,
@@ -316,7 +331,7 @@ def init_single_subject_wf(subject_id: str):
         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,
     )
@@ -347,11 +362,30 @@ def init_single_subject_wf(subject_id: str):
     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(
+                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():
@@ -395,6 +429,73 @@ def init_single_subject_wf(subject_id: str):
                 ]),
             ])  # 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(
+                grayord_density=config.workflow.cifti_output,
+                omp_nthreads=omp_nthreads,
+            )
+            resample_midthickness_wf = init_resample_midthickness_wf(
+                grayord_density=config.workflow.cifti_output,
+            )
+            ds_grayord_metrics_wf = init_ds_grayord_metrics_wf(
+                bids_root=bids_root,
+                output_dir=fmriprep_dir,
+                metrics=["curv", "thickness", "sulc"],
+                cifti_output=config.workflow.cifti_output,
+            )
+
+            workflow.connect([
+                (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)
 
@@ -421,8 +522,8 @@ def init_single_subject_wf(subject_id: str):
         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"""
@@ -481,7 +582,7 @@ def init_single_subject_wf(subject_id: str):
                     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,
@@ -561,7 +662,6 @@ def init_single_subject_wf(subject_id: str):
                 ('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"}',
@@ -609,6 +709,12 @@ def init_single_subject_wf(subject_id: str):
                 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)

fmriprep/workflows/bold/base.py

@@ -113,8 +113,6 @@ def init_bold_wf(
         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
@@ -235,7 +233,8 @@ def init_bold_wf(
                 "midthickness",
                 "pial",
                 "sphere_reg_fsLR",
-                "thickness",
+                "midthickness_fsLR",
+                "cortex_mask",
                 "anat_ribbon",
                 # Fieldmap registration
                 "fmap",
@@ -316,6 +315,7 @@ def init_bold_wf(
         omp_nthreads=omp_nthreads,
         name='bold_anat_wf',
     )
+    bold_anat_wf.inputs.inputnode.resolution = "native"
 
     workflow.connect([
         (inputnode, bold_native_wf, [
@@ -580,8 +580,9 @@ def init_bold_wf(
                 ("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, [