@@ -152,7 +152,18 @@ def init_single_subject_wf(subject_id: str):
152152 from niworkflows .utils .misc import fix_multi_T1w_source_name
153153 from niworkflows .utils .spaces import Reference
154154 from smriprep .workflows .anatomical import init_anat_fit_wf
155- from smriprep .workflows .outputs import init_template_iterator_wf
155+ from smriprep .workflows .outputs import (
156+ init_ds_anat_volumes_wf ,
157+ init_ds_grayord_metrics_wf ,
158+ init_ds_surface_metrics_wf ,
159+ init_template_iterator_wf ,
160+ )
161+ from smriprep .workflows .surfaces import (
162+ init_gifti_morphometrics_wf ,
163+ init_hcp_morphometrics_wf ,
164+ init_morph_grayords_wf ,
165+ init_resample_midthickness_wf ,
166+ )
156167
157168 from fmriprep .workflows .bold .base import init_bold_wf
158169
@@ -302,10 +313,14 @@ def init_single_subject_wf(subject_id: str):
302313 run_without_submitting = True ,
303314 )
304315
316+ bids_root = str (config .execution .bids_dir )
317+ fmriprep_dir = str (config .execution .fmriprep_dir )
318+ omp_nthreads = config .nipype .omp_nthreads
319+
305320 # Build the workflow
306321 anat_fit_wf = init_anat_fit_wf (
307- bids_root = str ( config . execution . bids_dir ) ,
308- output_dir = str ( config . execution . fmriprep_dir ) ,
322+ bids_root = bids_root ,
323+ output_dir = fmriprep_dir ,
309324 freesurfer = config .workflow .run_reconall ,
310325 hires = config .workflow .hires ,
311326 longitudinal = config .workflow .longitudinal ,
@@ -316,7 +331,7 @@ def init_single_subject_wf(subject_id: str):
316331 skull_strip_template = Reference .from_string (config .workflow .skull_strip_template )[0 ],
317332 spaces = spaces ,
318333 precomputed = anatomical_cache ,
319- omp_nthreads = config . nipype . omp_nthreads ,
334+ omp_nthreads = omp_nthreads ,
320335 sloppy = config .execution .sloppy ,
321336 skull_strip_fixed_seed = config .workflow .skull_strip_fixed_seed ,
322337 )
@@ -347,11 +362,30 @@ def init_single_subject_wf(subject_id: str):
347362 if config .workflow .level == "full" :
348363 if spaces .cached .get_spaces (nonstandard = False , dim = (3 ,)):
349364 template_iterator_wf = init_template_iterator_wf (spaces = spaces )
365+ ds_std_volumes_wf = init_ds_anat_volumes_wf (
366+ bids_root = bids_root ,
367+ output_dir = fmriprep_dir ,
368+ name = "ds_std_volumes_wf" ,
369+ )
350370 workflow .connect ([
351371 (anat_fit_wf , template_iterator_wf , [
352372 ('outputnode.template' , 'inputnode.template' ),
353373 ('outputnode.anat2std_xfm' , 'inputnode.anat2std_xfm' ),
354374 ]),
375+ (anat_fit_wf , ds_std_volumes_wf , [
376+ ('outputnode.t1w_valid_list' , 'inputnode.source_files' ),
377+ ("outputnode.t1w_preproc" , "inputnode.t1w_preproc" ),
378+ ("outputnode.t1w_mask" , "inputnode.t1w_mask" ),
379+ ("outputnode.t1w_dseg" , "inputnode.t1w_dseg" ),
380+ ("outputnode.t1w_tpms" , "inputnode.t1w_tpms" ),
381+ ]),
382+ (template_iterator_wf , ds_std_volumes_wf , [
383+ ("outputnode.std_t1w" , "inputnode.ref_file" ),
384+ ("outputnode.anat2std_xfm" , "inputnode.anat2std_xfm" ),
385+ ("outputnode.space" , "inputnode.space" ),
386+ ("outputnode.cohort" , "inputnode.cohort" ),
387+ ("outputnode.resolution" , "inputnode.resolution" ),
388+ ]),
355389 ]) # fmt:skip
356390
357391 if 'MNI152NLin2009cAsym' in spaces .get_spaces ():
@@ -395,6 +429,73 @@ def init_single_subject_wf(subject_id: str):
395429 ]),
396430 ]) # fmt:skip
397431
432+ # Create CIFTI morphometrics
433+ curv_wf = init_gifti_morphometrics_wf (morphometrics = ['curv' ], name = 'curv_wf' )
434+ hcp_morphometrics_wf = init_hcp_morphometrics_wf (omp_nthreads = omp_nthreads )
435+ morph_grayords_wf = init_morph_grayords_wf (
436+ grayord_density = config .workflow .cifti_output ,
437+ omp_nthreads = omp_nthreads ,
438+ )
439+ resample_midthickness_wf = init_resample_midthickness_wf (
440+ grayord_density = config .workflow .cifti_output ,
441+ )
442+ ds_grayord_metrics_wf = init_ds_grayord_metrics_wf (
443+ bids_root = bids_root ,
444+ output_dir = fmriprep_dir ,
445+ metrics = ["curv" , "thickness" , "sulc" ],
446+ cifti_output = config .workflow .cifti_output ,
447+ )
448+
449+ workflow .connect ([
450+ (anat_fit_wf , curv_wf , [
451+ ("outputnode.subject_id" , "inputnode.subject_id" ),
452+ ("outputnode.subjects_dir" , "inputnode.subjects_dir" ),
453+ ]),
454+ (anat_fit_wf , hcp_morphometrics_wf , [
455+ ("outputnode.subject_id" , "inputnode.subject_id" ),
456+ ("outputnode.thickness" , "inputnode.thickness" ),
457+ ("outputnode.sulc" , "inputnode.sulc" ),
458+ ("outputnode.midthickness" , "inputnode.midthickness" ),
459+ ]),
460+ (curv_wf , hcp_morphometrics_wf , [
461+ ("outputnode.curv" , "inputnode.curv" ),
462+ ]),
463+ (anat_fit_wf , resample_midthickness_wf , [
464+ ('outputnode.midthickness' , 'inputnode.midthickness' ),
465+ (
466+ f"outputnode.sphere_reg_{ 'msm' if msm_sulc else 'fsLR' } ,
467+ "inputnode.sphere_reg_fsLR" ,
468+ ),
469+ ]),
470+ (anat_fit_wf , morph_grayords_wf , [
471+ ("outputnode.midthickness" , "inputnode.midthickness" ),
472+ (
473+ f'outputnode.sphere_reg_{ "msm" if msm_sulc else "fsLR" } ,
474+ 'inputnode.sphere_reg_fsLR' ,
475+ ),
476+ ]),
477+ (hcp_morphometrics_wf , morph_grayords_wf , [
478+ ("outputnode.curv" , "inputnode.curv" ),
479+ ("outputnode.thickness" , "inputnode.thickness" ),
480+ ("outputnode.sulc" , "inputnode.sulc" ),
481+ ("outputnode.roi" , "inputnode.roi" ),
482+ ]),
483+ (resample_midthickness_wf , morph_grayords_wf , [
484+ ('outputnode.midthickness_fsLR' , 'inputnode.midthickness_fsLR' ),
485+ ]),
486+ (anat_fit_wf , ds_grayord_metrics_wf , [
487+ ('outputnode.t1w_valid_list' , 'inputnode.source_files' ),
488+ ]),
489+ (morph_grayords_wf , ds_grayord_metrics_wf , [
490+ ("outputnode.curv_fsLR" , "inputnode.curv" ),
491+ ("outputnode.curv_metadata" , "inputnode.curv_metadata" ),
492+ ("outputnode.thickness_fsLR" , "inputnode.thickness" ),
493+ ("outputnode.thickness_metadata" , "inputnode.thickness_metadata" ),
494+ ("outputnode.sulc_fsLR" , "inputnode.sulc" ),
495+ ("outputnode.sulc_metadata" , "inputnode.sulc_metadata" ),
496+ ]),
497+ ]) # fmt:skip
498+
398499 if config .workflow .anat_only :
399500 return clean_datasinks (workflow )
400501
@@ -421,8 +522,8 @@ def init_single_subject_wf(subject_id: str):
421522 fmap_wf = init_fmap_preproc_wf (
422523 debug = "fieldmaps" in config .execution .debug ,
423524 estimators = fmap_estimators ,
424- omp_nthreads = config . nipype . omp_nthreads ,
425- output_dir = str ( config . execution . fmriprep_dir ) ,
525+ omp_nthreads = omp_nthreads ,
526+ output_dir = fmriprep_dir ,
426527 subject = subject_id ,
427528 )
428529 fmap_wf .__desc__ = f"""
@@ -481,7 +582,7 @@ def init_single_subject_wf(subject_id: str):
481582 s .metadata for s in estimator .sources if s .suffix in ("bold" , "sbref" )
482583 ]
483584 syn_preprocessing_wf = init_syn_preprocessing_wf (
484- omp_nthreads = config . nipype . omp_nthreads ,
585+ omp_nthreads = omp_nthreads ,
485586 debug = config .execution .sloppy ,
486587 auto_bold_nss = True ,
487588 t1w_inversion = False ,
@@ -561,7 +662,6 @@ def init_single_subject_wf(subject_id: str):
561662 ('outputnode.white' , 'inputnode.white' ),
562663 ('outputnode.pial' , 'inputnode.pial' ),
563664 ('outputnode.midthickness' , 'inputnode.midthickness' ),
564- ('outputnode.thickness' , 'inputnode.thickness' ),
565665 ('outputnode.anat_ribbon' , 'inputnode.anat_ribbon' ),
566666 (
567667 f'outputnode.sphere_reg_{ "msm" if msm_sulc else "fsLR" } ,
@@ -609,6 +709,12 @@ def init_single_subject_wf(subject_id: str):
609709 workflow .connect ([
610710 (select_MNI6_xfm , bold_wf , [("anat2std_xfm" , "inputnode.anat2mni6_xfm" )]),
611711 (select_MNI6_tpl , bold_wf , [("brain_mask" , "inputnode.mni6_mask" )]),
712+ (hcp_morphometrics_wf , bold_wf , [
713+ ("outputnode.roi" , "inputnode.cortex_mask" ),
714+ ]),
715+ (resample_midthickness_wf , bold_wf , [
716+ ('outputnode.midthickness_fsLR' , 'inputnode.midthickness_fsLR' ),
717+ ]),
612718 ]) # fmt:skip
613719
614720 return clean_datasinks (workflow )
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