Merge remote-tracking branch 'upstream/master' into rel/23.2.0

Author: effigies

.circleci/ds005_fasttrack_outputs.txt

@@ -23,16 +23,12 @@ 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/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
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz
-sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
@@ -45,16 +41,12 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json

.circleci/ds005_outputs.txt

@@ -43,16 +43,12 @@ 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/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
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz
-sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
@@ -65,16 +61,12 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
 sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -51,16 +51,12 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 sub-01/func
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json

.circleci/ds005_partial_outputs.txt

@@ -73,16 +73,12 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
 sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 sub-01/func
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json
-sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
 sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json

.circleci/ds210_fasttrack_outputs.txt

@@ -31,8 +31,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.json
 sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.json
 sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.nii.gz
-sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.json
-sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
@@ -45,8 +43,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg
 sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
 sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
-sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
-sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json

.circleci/ds210_outputs.txt

@@ -41,8 +41,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.json
 sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.json
 sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.nii.gz
-sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.json
-sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
@@ -55,8 +53,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg
 sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
 sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
 sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
-sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
-sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
 sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json

.github/workflows/contrib.yml

@@ -32,7 +32,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version

.github/workflows/pre-release.yml

@@ -45,7 +45,7 @@ jobs:
       - name: Install dependencies
         run: .maint/ci/install_dependencies.sh
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version

.github/workflows/stable.yml

@@ -48,7 +48,7 @@ jobs:
       - name: Install dependencies
         run: .maint/ci/install_dependencies.sh
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version

docker/files/freesurfer7.3.2-exclude.txt

@@ -802,7 +802,6 @@ freesurfer/mni/bin/mincreshape
 freesurfer/mni/bin/mincstats
 freesurfer/mni/bin/minctoecat
 freesurfer/mni/bin/minctoraw
-freesurfer/mni/bin/minctracc
 freesurfer/mni/bin/mincview
 freesurfer/mni/bin/mincwindow
 freesurfer/mni/bin/mnc2nii