Merge branch 'upstream/maint/22.0.x'

.circleci/config.yml

@@ -481,6 +481,9 @@ jobs:
             sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_partial
             sudo cp -a /tmp/${DATASET}/work /tmp/${DATASET}/work_bids
             sudo rm -rf /tmp/${DATASET}/work_partial/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf
+            # Nipype sometimes fails to pick up when the base directory changes
+            # This is a cheap workflow, so let's not fuss
+            sudo rm -rf /tmp/${DATASET}/work /tmp/${DATASET}/work_bids/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf || true
       - run:
           name: Checking outputs of full fMRIPrep run
           command: |

.circleci/ds005_bids_outputs.txt

@@ -32,41 +32,21 @@ bids/sub-01/anat/sub-01_hemi-R_smoothwm.surf.gii
 bids/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
 bids/sub-01/anat/sub-01_label-GM_probseg.nii.gz
 bids/sub-01/anat/sub-01_label-WM_probseg.nii.gz
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_dseg.nii.gz
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
-bids/sub-01/anat/sub-01_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
-bids/sub-01/fmap
-bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff0_fieldmap.nii.gz
-bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-coeff1_fieldmap.nii.gz
-bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
-bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.json
-bids/sub-01/fmap/sub-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 bids/sub-01/func
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
-bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii
+bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json
 bids/sub-01.html

.circleci/ds005_legacy_partial_outputs.txt

@@ -63,17 +63,17 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseri
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L_bold.func.gii
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-L_bold.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R_bold.func.gii
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsaverage5_hemi-R_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsnative_bold.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsnative_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsaverage5_bold.json
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.func.gii
+fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-L_bold.func.gii
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-L_bold.json
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R_bold.func.gii
-fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsnative_hemi-R_bold.json
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
 fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz

.circleci/ds210_fasttrack_outputs.txt

@@ -14,6 +14,9 @@ fmriprep/sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.
 fmriprep/sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
 fmriprep/sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-02/func
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_boldref.nii.gz
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-brain_mask.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-brain_mask.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-confounds_timeseries.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-confounds_timeseries.tsv
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json
@@ -24,6 +27,8 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-T1w_to-scanner_mode-image_xfm.txt
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz

.circleci/ds210_outputs.txt

@@ -33,6 +33,9 @@ fmriprep/sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.
 fmriprep/sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
 fmriprep/sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
 fmriprep/sub-02/func
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_boldref.nii.gz
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-brain_mask.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-brain_mask.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-confounds_timeseries.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_desc-confounds_timeseries.tsv
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json
@@ -43,6 +46,8 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-T1w_mode-image_xfm.txt
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-T1w_to-scanner_mode-image_xfm.txt
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
+fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
 fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz

CHANGES.rst

@@ -56,9 +56,25 @@ any issues you find.
   * CI: Touch up CircleCI configuration (#2764)
   * CI: Update package builds to use python -m build (#2746)
 
+21.0.4 (September 29, 2022)
+===========================
+Bug-fix release in the 21.0.x series.
+
+  * FIX: Output brain mask and boldref in BOLD space if individual echos requested (#2852)
+  * FIX: Check for empty ACompCor results before trying to rename (#2851)
+  * CI: Fix non-fasttrack outputs for maint/21.0.x (#2866)
+
+21.0.3 (September 6, 2022)
+==========================
+Bug-fix release in the 21.0.x series.
+
+This release includes a fix for `--bids-filter-file` not respecting `sbref` filtering.
+
+  * FIX: Filter sbrefs by BIDS filters if available (#2843)
+
 21.0.2 (April 21, 2022)
 =======================
-Bug-fix releaase in the 21.0.x series.
+Bug-fix release in the 21.0.x series.
 
 This release includes a few bug-fixes for susceptibility distortion correction (SDC) and multi-echo (ME).
 A few notable fixes include:

docs/outputs.rst

@@ -260,6 +260,8 @@ Then the output will include::
 
   sub-01/
     func/
+      sub-01_task-rest_boldref.nii.gz
+      sub-01_task-rest_desc-brain_mask.nii.gz
       sub-01_task-rest_echo-1_desc-preproc_bold.nii.gz
       sub-01_task-rest_echo-2_desc-preproc_bold.nii.gz
       sub-01_task-rest_echo-3_desc-preproc_bold.nii.gz

fmriprep/workflows/bold/outputs.py

@@ -280,7 +280,8 @@ def init_func_derivatives_wf(
     ])
     # fmt:on
 
-    if nonstd_spaces.intersection(('func', 'run', 'bold', 'boldref', 'sbref')):
+    bold_output = nonstd_spaces.intersection(('func', 'run', 'bold', 'boldref', 'sbref'))
+    if bold_output:
         ds_bold_native = pe.Node(
             DerivativesDataSink(
                 base_directory=output_dir,
@@ -294,6 +295,15 @@ def init_func_derivatives_wf(
             run_without_submitting=True,
             mem_gb=DEFAULT_MEMORY_MIN_GB,
         )
+        # fmt: off
+        workflow.connect([
+            (inputnode, ds_bold_native, [('source_file', 'source_file'),
+                                         ('bold_native', 'in_file')]),
+        ])
+        # fmt:on
+
+    # Save masks and boldref if we're going to save either orig BOLD series or echos
+    if bold_output or multiecho and config.execution.me_output_echos:
         ds_bold_native_ref = pe.Node(
             DerivativesDataSink(
                 base_directory=output_dir,
@@ -319,8 +329,6 @@ def init_func_derivatives_wf(
         )
         # fmt:off
         workflow.connect([
-            (inputnode, ds_bold_native, [('source_file', 'source_file'),
-                                         ('bold_native', 'in_file')]),
             (inputnode, ds_bold_native_ref, [('source_file', 'source_file'),
                                              ('bold_native_ref', 'in_file')]),
             (inputnode, ds_bold_mask_native, [('source_file', 'source_file'),