Merge tag '23.2.3'

23.2.3 (May 20, 2024)

Bug fix release in the 23.2.x series.

Writes brain masks in ``space-boldref`` with ``--level minimal``,
bringing behavior in line with documentation.

* FIX: Write out boldref-space brain mask with minimal level (#3292)

Author: effigies

.circleci/ds005_fasttrack_outputs.txt

@@ -23,6 +23,8 @@ 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
@@ -41,6 +43,8 @@ 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

.circleci/ds005_outputs.txt

@@ -43,6 +43,8 @@ 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
@@ -61,6 +63,8 @@ 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

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -51,6 +51,8 @@ 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

.circleci/ds005_partial_outputs.txt

@@ -73,6 +73,8 @@ 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

CHANGES.rst

@@ -1,3 +1,13 @@
+23.2.3 (May 20, 2024)
+=====================
+Bug fix release in the 23.2.x series.
+
+Writes brain masks in ``space-boldref`` with ``--level minimal``,
+bringing behavior in line with documentation.
+
+* FIX: Write out boldref-space brain mask with minimal level (#3292)
+
+
 23.2.2 (May 06, 2024)
 =====================
 Bug fix release in the 23.2.x series.

fmriprep/workflows/bold/base.py

@@ -326,11 +326,6 @@ def init_bold_wf(
         ds_bold_native_wf.inputs.inputnode.source_files = bold_series
 
         workflow.connect([
-            (bold_fit_wf, ds_bold_native_wf, [
-                ('outputnode.bold_mask', 'inputnode.bold_mask'),
-                ('outputnode.motion_xfm', 'inputnode.motion_xfm'),
-                ('outputnode.boldref2fmap_xfm', 'inputnode.boldref2fmap_xfm'),
-            ]),
             (bold_native_wf, ds_bold_native_wf, [
                 ('outputnode.bold_native', 'inputnode.bold'),
                 ('outputnode.bold_echos', 'inputnode.bold_echos'),

fmriprep/workflows/bold/fit.py

@@ -47,6 +47,7 @@
 # BOLD workflows
 from .hmc import init_bold_hmc_wf
 from .outputs import (
+    init_ds_boldmask_wf,
     init_ds_boldref_wf,
     init_ds_hmc_wf,
     init_ds_registration_wf,
@@ -472,6 +473,13 @@ def init_bold_fit_wf(
             desc='coreg',
             name='ds_coreg_boldref_wf',
         )
+        ds_boldmask_wf = init_ds_boldmask_wf(
+            bids_root=layout.root,
+            output_dir=config.execution.fmriprep_dir,
+            desc='brain',
+            name='ds_boldmask_wf',
+        )
+        ds_boldmask_wf.inputs.inputnode.source_files = [bold_file]
 
         workflow.connect([
             (hmcref_buffer, fmapref_buffer, [('boldref', 'boldref_files')]),
@@ -480,6 +488,7 @@ def init_bold_fit_wf(
                 ('in_file', 'inputnode.source_files'),
             ]),
             (ds_coreg_boldref_wf, regref_buffer, [('outputnode.boldref', 'boldref')]),
+            (ds_boldmask_wf, regref_buffer, [('outputnode.boldmask', 'boldmask')]),
             (fmapref_buffer, func_fit_reports_wf, [('out', 'inputnode.sdc_boldref')]),
         ])  # fmt:skip
 
@@ -562,8 +571,8 @@ def init_bold_fit_wf(
                 (unwarp_wf, ds_coreg_boldref_wf, [
                     ('outputnode.corrected', 'inputnode.boldref'),
                 ]),
-                (unwarp_wf, regref_buffer, [
-                    ('outputnode.corrected_mask', 'boldmask'),
+                (unwarp_wf, ds_boldmask_wf, [
+                    ('outputnode.corrected_mask', 'inputnode.boldmask'),
                 ]),
                 (fmap_select, func_fit_reports_wf, [('fmap_ref', 'inputnode.fmap_ref')]),
                 (fmap_select, summary, [('sdc_method', 'distortion_correction')]),
@@ -579,8 +588,8 @@ def init_bold_fit_wf(
                 (enhance_boldref_wf, ds_coreg_boldref_wf, [
                     ('outputnode.bias_corrected_file', 'inputnode.boldref'),
                 ]),
-                (enhance_boldref_wf, regref_buffer, [
-                    ('outputnode.mask_file', 'boldmask'),
+                (enhance_boldref_wf, ds_boldmask_wf, [
+                    ('outputnode.mask_file', 'inputnode.boldmask'),
                 ]),
             ])
             # fmt:on

fmriprep/workflows/bold/outputs.py

@@ -29,6 +29,7 @@
 from nipype.pipeline import engine as pe
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 from niworkflows.utils.images import dseg_label
+from smriprep.workflows.outputs import _bids_relative
 
 from fmriprep import config
 from fmriprep.config import DEFAULT_MEMORY_MIN_GB
@@ -471,6 +472,50 @@ def init_ds_boldref_wf(
     return workflow
 
 
+def init_ds_boldmask_wf(
+    *,
+    bids_root,
+    output_dir,
+    desc: str,
+    name='ds_boldmask_wf',
+) -> pe.Workflow:
+    """Write out a BOLD mask."""
+    workflow = pe.Workflow(name=name)
+
+    inputnode = pe.Node(
+        niu.IdentityInterface(fields=['source_files', 'boldmask']),
+        name='inputnode',
+    )
+    outputnode = pe.Node(niu.IdentityInterface(fields=['boldmask']), name='outputnode')
+
+    raw_sources = pe.Node(niu.Function(function=_bids_relative), name='raw_sources')
+    raw_sources.inputs.bids_root = bids_root
+
+    ds_boldmask = pe.Node(
+        DerivativesDataSink(
+            base_directory=output_dir,
+            desc=desc,
+            suffix='mask',
+            compress=True,
+            dismiss_entities=dismiss_echo(),
+        ),
+        name='ds_boldmask',
+        run_without_submitting=True,
+    )
+
+    workflow.connect([
+        (inputnode, raw_sources, [('source_files', 'in_files')]),
+        (inputnode, ds_boldmask, [
+            ('boldmask', 'in_file'),
+            ('source_files', 'source_file'),
+        ]),
+        (raw_sources, ds_boldmask, [('out', 'RawSources')]),
+        (ds_boldmask, outputnode, [('out_file', 'boldmask')]),
+    ])  # fmt:skip
+
+    return workflow
+
+
 def init_ds_registration_wf(
     *,
     bids_root: str,
@@ -592,7 +637,6 @@ def init_ds_bold_native_wf(
             fields=[
                 'source_files',
                 'bold',
-                'bold_mask',
                 'bold_echos',
                 't2star',
                 # Transforms previously used to generate the outputs
@@ -619,27 +663,6 @@ def init_ds_bold_native_wf(
         ]),
     ])  # fmt:skip
 
-    # Masks should be output if any other derivatives are output
-    ds_bold_mask = pe.Node(
-        DerivativesDataSink(
-            base_directory=output_dir,
-            desc='brain',
-            suffix='mask',
-            compress=True,
-            dismiss_entities=dismiss_echo(),
-        ),
-        name='ds_bold_mask',
-        run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB,
-    )
-    workflow.connect([
-        (inputnode, ds_bold_mask, [
-            ('source_files', 'source_file'),
-            ('bold_mask', 'in_file'),
-        ]),
-        (sources, ds_bold_mask, [('out', 'Sources')]),
-    ])  # fmt:skip
-
     if bold_output:
         ds_bold = pe.Node(
             DerivativesDataSink(