Merge remote-tracking branch 'upstream/master' into flexible-cifti

Author: tsalo

.circleci/ds005_fasttrack_outputs.txt

@@ -14,14 +14,14 @@ 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_desc-reg_sphere.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_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_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
 sub-01/func
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz

.circleci/ds005_outputs.txt

@@ -21,20 +21,20 @@ sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
 sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
 sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
-sub-01/anat/sub-01_hemi-L_desc-reg_sphere.surf.gii
 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_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-L_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 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_desc-reg_sphere.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_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
 sub-01/anat/sub-01_hemi-R_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_sulc.shape.gii
 sub-01/anat/sub-01_hemi-R_thickness.shape.gii

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -14,14 +14,14 @@ 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_desc-reg_sphere.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_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_hemi-R_space-fsaverage_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

.circleci/ds005_partial_outputs.txt

@@ -23,20 +23,20 @@ sub-01/anat/sub-01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
 sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 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_desc-reg_sphere.surf.gii
 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_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-L_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 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_desc-reg_sphere.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_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
 sub-01/anat/sub-01_hemi-R_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_sulc.shape.gii
 sub-01/anat/sub-01_hemi-R_thickness.shape.gii

env.yml

@@ -12,8 +12,6 @@ dependencies:
   - mkl-service=2.4.0
   # git-annex for templateflow users with DataLad superdatasets
   - git-annex=*=alldep*
-  # ANTs is linked against libitk 5.3 but does not pin the version
-  - libitk=5.3
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
   - scipy=1.13

fmriprep/workflows/base.py

@@ -387,10 +387,10 @@ def init_single_subject_wf(subject_id: str):
                 ]),
                 (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'),

fmriprep/workflows/bold/outputs.py

@@ -441,7 +441,7 @@ def init_ds_boldref_wf(
         BIDSURI(
             numinputs=1,
             dataset_links=config.execution.dataset_links,
-            out_dir=str(config.execution.fmriprep_dir.absolute()),
+            out_dir=str(output_dir),
         ),
         name='sources',
     )
@@ -490,7 +490,7 @@ def init_ds_boldmask_wf(
         BIDSURI(
             numinputs=1,
             dataset_links=config.execution.dataset_links,
-            out_dir=str(config.execution.fmriprep_dir.absolute()),
+            out_dir=str(output_dir),
         ),
         name='sources',
     )
@@ -540,7 +540,7 @@ def init_ds_registration_wf(
         BIDSURI(
             numinputs=1,
             dataset_links=config.execution.dataset_links,
-            out_dir=str(config.execution.fmriprep_dir.absolute()),
+            out_dir=str(output_dir),
         ),
         name='sources',
     )
@@ -590,7 +590,7 @@ def init_ds_hmc_wf(
         BIDSURI(
             numinputs=1,
             dataset_links=config.execution.dataset_links,
-            out_dir=str(config.execution.fmriprep_dir.absolute()),
+            out_dir=str(output_dir),
         ),
         name='sources',
     )
@@ -655,7 +655,7 @@ def init_ds_bold_native_wf(
         BIDSURI(
             numinputs=3,
             dataset_links=config.execution.dataset_links,
-            out_dir=str(config.execution.fmriprep_dir.absolute()),
+            out_dir=str(output_dir),
         ),
         name='sources',
     )
@@ -783,7 +783,7 @@ def init_ds_volumes_wf(
         BIDSURI(
             numinputs=6,
             dataset_links=config.execution.dataset_links,
-            out_dir=str(config.execution.fmriprep_dir.absolute()),
+            out_dir=str(output_dir),
         ),
         name='sources',
     )

fmriprep/workflows/bold/resampling.py

@@ -148,7 +148,7 @@ def init_bold_surf_wf(
         BIDSURI(
             numinputs=1,
             dataset_links=config.execution.dataset_links,
-            out_dir=str(config.execution.fmriprep_dir.absolute()),
+            out_dir=str(output_dir),
         ),
         name='surfs_sources',
     )