Merge remote-tracking branch 'upstream/maint/24.1.x'

Author: effigies

CHANGES.rst

@@ -1,27 +1,36 @@
+24.1.2 (To be determined)
+=========================
+Bug fix release in the 24.1.x series.
+
+* FIX: Ensure fieldmap is resampled correctly in report (#3387)
+
+
 24.1.1 (October 10, 2024)
 =========================
 Bug fix release in the 24.1.x series.
 
 Precomputed functional derivatives were not being correctly detected,
 and a couple fixes for rare issues.
 
-  * FIX: Remove checks for unit zooms and symmetric rotations in template warp (#3376)
-  * FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
-  * FIX: Repair search for precomputed bold references (#3370)
-  * FIX: Repair search for precomputed transforms (#3369)
+* FIX: Remove checks for unit zooms and symmetric rotations in template warp (#3376)
+* FIX: Stop excluding FS minc_modify_header used during fallback registration (#3372)
+* FIX: Repair search for precomputed bold references (#3370)
+* FIX: Repair search for precomputed transforms (#3369)
+
 
 24.1.0 (September 16, 2024)
 ===========================
 New feature release in the 24.1.x series.
 
 Handling of gradient echo fieldmaps is improved.
 
-  * FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257)
-  * RF: Adapt to less T1w-centric smriprep (#3333)
-  * RF: Use acres over vendored data loader (#3323)
-  * DOC: Add benchmark page (#3312)
-  * MAINT: Move to tox to simplify test/CI setup (#3326)
-  * CI: Fix expected outputs for fieldmaps (#3321)
+* FIX: Select volumetric dseg.tsv from recent TemplateFlow releases (#3257)
+* RF: Adapt to less T1w-centric smriprep (#3333)
+* RF: Use acres over vendored data loader (#3323)
+* DOC: Add benchmark page (#3312)
+* MAINT: Move to tox to simplify test/CI setup (#3326)
+* CI: Fix expected outputs for fieldmaps (#3321)
+
 
 24.0.1 (July 16, 2024)
 ======================

fmriprep/cli/parser.py

@@ -105,9 +105,6 @@ def _to_gb(value):
         units = value[len(digits) :] or 'M'
         return int(digits) * scale[units[0]]
 
-    def _drop_sub(value):
-        return value[4:] if value.startswith('sub-') else value
-
     def _process_value(value):
         import bids
 
@@ -205,7 +202,7 @@ def _slice_time_ref(value, parser):
         '--participant_label',
         action='store',
         nargs='+',
-        type=_drop_sub,
+        type=lambda label: label.removeprefix('sub-'),
         help='A space delimited list of participant identifiers or a single '
         'identifier (the sub- prefix can be removed)',
     )

fmriprep/reports/core.py

@@ -76,9 +76,12 @@ def generate_reports(
 
     if isinstance(subject_list, str):
         subject_list = [subject_list]
+    if isinstance(session_list, str):
+        session_list = [session_list]
 
     errors = []
     for subject_label in subject_list:
+        subject_label = subject_label.removeprefix('sub-')
         # The number of sessions is intentionally not based on session_list but
         # on the total number of sessions, because I want the final derivatives
         # folder to be the same whether sessions were run one at a time or all-together.
@@ -95,7 +98,7 @@ def generate_reports(
         else:
             # Beyond a threshold, we separate the anatomical report from the functional.
             bootstrap_file = data.load('reports-spec-anat.yml')
-            html_report = f'sub-{subject_label.lstrip("sub-")}_anat.html'
+            html_report = f'sub-{subject_label}_anat.html'
 
         report_error = run_reports(
             output_dir,
@@ -121,12 +124,11 @@ def generate_reports(
                     subject=subject_label, **filters
                 )
 
-            # Drop ses- prefixes
-            session_list = [ses[4:] if ses.startswith('ses-') else ses for ses in session_list]
+            session_list = [ses.removeprefix('ses-') for ses in session_list]
 
             for session_label in session_list:
                 bootstrap_file = data.load('reports-spec-func.yml')
-                html_report = f'sub-{subject_label.lstrip("sub-")}_ses-{session_label}_func.html'
+                html_report = f'sub-{subject_label}_ses-{session_label}_func.html'
 
                 report_error = run_reports(
                     output_dir,

fmriprep/utils/bids.py

@@ -217,7 +217,7 @@ def validate_input_dir(exec_env, bids_dir, participant_label, need_T1w=True):
     # Limit validation only to data from requested participants
     if participant_label:
         all_subs = {s.name[4:] for s in bids_dir.glob('sub-*')}
-        selected_subs = {s[4:] if s.startswith('sub-') else s for s in participant_label}
+        selected_subs = {s.removeprefix('sub-') for s in participant_label}
         bad_labels = selected_subs.difference(all_subs)
         if bad_labels:
             error_msg = (

fmriprep/workflows/bold/outputs.py

@@ -316,14 +316,26 @@ def init_func_fit_reports_wf(
             mem_gb=1,
         )
 
+        fmap_boldref = pe.Node(
+            ApplyTransforms(
+                dimension=3,
+                default_value=0,
+                float=True,
+                invert_transform_flags=[True],
+                interpolation='LanczosWindowedSinc',
+            ),
+            name='fmap_boldref',
+            mem_gb=1,
+        )
+
         # SDC1
         sdcreg_report = pe.Node(
             FieldmapReportlet(
                 reference_label='BOLD reference',
                 moving_label='Fieldmap reference',
                 show='both',
             ),
-            name='sdecreg_report',
+            name='sdcreg_report',
             mem_gb=0.1,
         )
 
@@ -360,19 +372,23 @@ def init_func_fit_reports_wf(
             name='ds_sdc_report',
         )
 
-        # fmt:off
         workflow.connect([
             (inputnode, fmapref_boldref, [
                 ('fmap_ref', 'input_image'),
                 ('coreg_boldref', 'reference_image'),
                 ('boldref2fmap_xfm', 'transforms'),
             ]),
+            (inputnode, fmap_boldref, [
+                ('fieldmap', 'input_image'),
+                ('coreg_boldref', 'reference_image'),
+                ('boldref2fmap_xfm', 'transforms'),
+            ]),
             (inputnode, sdcreg_report, [
                 ('sdc_boldref', 'reference'),
-                ('fieldmap', 'fieldmap'),
                 ('bold_mask', 'mask'),
             ]),
             (fmapref_boldref, sdcreg_report, [('output_image', 'moving')]),
+            (fmap_boldref, sdcreg_report, [('output_image', 'fieldmap')]),
             (inputnode, ds_sdcreg_report, [('source_file', 'source_file')]),
             (sdcreg_report, ds_sdcreg_report, [('out_report', 'in_file')]),
             (inputnode, sdc_report, [
@@ -382,8 +398,7 @@ def init_func_fit_reports_wf(
             (boldref_wm, sdc_report, [('output_image', 'wm_seg')]),
             (inputnode, ds_sdc_report, [('source_file', 'source_file')]),
             (sdc_report, ds_sdc_report, [('out_report', 'in_file')]),
-        ])
-        # fmt:on
+        ])  # fmt:skip
 
     # EPI-T1 registration
     # Resample T1w image onto EPI-space