Merge tag '25.2.0'

25.2.0 (September 25, 2025)

The first release of the 25.2.x series.

This release synchronizes with downstream dependencies, as well as
leverages TemplateFlow to retrieve intermediate transforms used during multi-step registration.

If you are reusing a previous TemplateFlow cache (which may be the case if running with
Apptainer / Singularity), you will need to clear or update your cache to ensure these new files
are available.

Thanks to @LuciMoore for the contribution!

Documentation
  * DOC: MCRIBS and surf recon methods chosen based on age (#485)

Enhancements
  * ENH: Retrieve transforms with templateflow (#486)
  * ENH: Save cortex mask (#487)
  * ENH: Add multiverse output layout (#481)

Bug Fixes
  * FIX: Default to grid-constant when resampling BOLD to output spaces
  * FIX: Propagate error code if pipeline run is unsuccessful

Author: mgxd

CHANGES.md

@@ -1,3 +1,28 @@
+25.2.0 (September 25, 2025)
+===========================
+The first release of the 25.2.x series.
+
+This release synchronizes with downstream dependencies, as well as
+leverages TemplateFlow to retrieve intermediate transforms used during multi-step registration.
+
+If you are reusing a previous TemplateFlow cache (which may be the case if running with
+Apptainer / Singularity), you will need to clear or update your cache to ensure these new files
+are available.
+
+Thanks to @LuciMoore for the contribution!
+
+### Documentation
+  * DOC: MCRIBS and surf recon methods chosen based on age (#485)
+
+### Enhancements
+  * ENH: Retrieve transforms with templateflow (#486)
+  * ENH: Save cortex mask (#487)
+  * ENH: Add multiverse output layout (#481)
+
+### Bug Fixes
+  * FIX: Default to grid-constant when resampling BOLD to output spaces
+  * FIX: Propagate error code if pipeline run is unsuccessful
+
 25.1.2 (August 28, 2025)
 ========================
 A patch release in the 25.1.x series.

nibabies/cli/run.py

@@ -104,6 +104,7 @@ def main():
             nibabies_wf.run(**_plugin)
         except Exception as e:
             config.loggers.workflow.critical('nibabies failed: %s', e)
+            exitcode = 1
             raise
         else:
             config.loggers.workflow.log(25, 'nibabies finished successfully!')
@@ -147,7 +148,7 @@ def main():
             add_hash = config.execution.output_layout == 'multiverse'
 
             # Generate reports phase
-            generate_reports(
+            failed_reports = generate_reports(
                 config.execution.unique_labels,
                 config.execution.nibabies_dir,
                 config.execution.run_uuid,
@@ -161,6 +162,16 @@ def main():
             )
             write_bidsignore(config.execution.nibabies_dir)
 
+            if failed_reports:
+                msg = (
+                    'Report generation was not successful for the following participants '
+                    f': {", ".join(failed_reports)}.'
+                )
+                config.loggers.cli.error(msg)
+
+            if int(exitcode) or failed_reports:
+                sys.exit(1)
+
 
 if __name__ == '__main__':
     raise RuntimeError(

nibabies/interfaces/resampling.py

@@ -62,8 +62,15 @@ class ResampleSeriesInputSpec(TraitedSpec):
     num_threads = traits.Int(1, usedefault=True, desc='Number of threads to use for resampling')
     output_data_type = traits.Str('float32', usedefault=True, desc='Data type of output image')
     order = traits.Int(3, usedefault=True, desc='Order of interpolation (0=nearest, 3=cubic)')
-    mode = traits.Str(
+    mode = traits.Enum(
+        'grid-constant',
+        'nearest',
         'constant',
+        'mirror',
+        'reflect',
+        'wrap',
+        'grid-mirror',
+        'grid-wrap',
         usedefault=True,
         desc='How data is extended beyond its boundaries. '
         'See scipy.ndimage.map_coordinates for more details.',
@@ -561,7 +568,7 @@ def resample_image(
         hmc = []
 
     # Retrieve the RAS coordinates of the target space
-    coordinates = nt.base.SpatialReference.factory(target).ndcoords.astype('f4').T
+    coordinates = nt.base.SpatialReference.factory(target).ndcoords.astype('f4')
 
     # We will operate in voxel space, so get the source affine
     vox2ras = source.affine

nibabies/utils/transforms.py

@@ -20,7 +20,7 @@ def load_transforms(xfm_paths: list[Path], inverse: list[bool]) -> nt.base.Trans
         path = Path(path)
         if path.suffix == '.h5':
             # Load as a TransformChain
-            xfm = nt.manip.load(path)
+            xfm = nt.manip.load(path, fmt='h5')
         else:
             xfm = nt.linear.load(path)
         if inv:

nibabies/utils/viz.py

@@ -211,11 +211,12 @@ def plot_carpet(
         legend = False
 
     else:  # Volumetric NIfTI
-        from nilearn._utils import check_niimg_4d
         from nilearn._utils.niimg import _safe_get_data
+        from nilearn._utils.niimg_conversions import check_niimg
 
-        img_nii = check_niimg_4d(
+        img_nii = check_niimg(
             img,
+            ensure_ndim=4,
             dtype='auto',
         )
         func_data = _safe_get_data(img_nii, ensure_finite=True)

pyproject.toml

@@ -20,22 +20,22 @@ license = {file = "LICENSE"}
 requires-python = ">=3.10"
 dependencies = [
     "acres",
-    "nibabel >= 5.0.0",
-    "nipype >= 1.8.5",
-    "nireports >= 23.2.0",
+    "nibabel >= 5.1.0",
+    "nipype >= 1.9.0",
+    "nireports >= 25.3.0",
     "nitime",
-    "nitransforms >= 24.1.1",
+    "nitransforms >= 25.0.1",
     "niworkflows >= 1.14.1",
-    "numpy >= 1.21.0",
+    "numpy >= 2.0",
     "packaging",
     "pandas < 3",
     "psutil >= 5.4",
     "pybids >= 0.15.0",
     "requests",
-    "sdcflows >= 2.13.0",
+    "sdcflows >= 2.14.0",
     "smriprep >= 0.19.1",
     "tedana >= 23.0.2",
-    "templateflow >= 24.2.0",
+    "templateflow >= 25.0.3",
     "toml",
     "typing_extensions; python_version<'3.11'",
 ]

requirements.txt

@@ -204,18 +204,20 @@ nipype==1.10.0
     #   niworkflows
     #   sdcflows
     #   smriprep
-nireports==25.2.0
+nireports==25.3.0
     # via
     #   nibabies (pyproject.toml)
     #   sdcflows
+    #   smriprep
 nitime==0.11
     # via nibabies (pyproject.toml)
-nitransforms==24.1.2
+nitransforms==25.0.1
     # via
     #   nibabies (pyproject.toml)
     #   niworkflows
     #   sdcflows
-niworkflows==1.13.4
+    #   smriprep
+niworkflows==1.14.1
     # via
     #   nibabies (pyproject.toml)
     #   sdcflows
@@ -265,7 +267,6 @@ packaging==25.0
     #   nilearn
     #   nipype
     #   niworkflows
-    #   pooch
     #   scikit-image
     #   smriprep
 pandas==2.2.3
@@ -289,11 +290,7 @@ pillow==11.2.1
     #   matplotlib
     #   scikit-image
 platformdirs==4.3.8
-    # via
-    #   datalad
-    #   pooch
-pooch==1.8.2
-    # via nibabies (pyproject.toml)
+    # via datalad
 prov==2.0.2
     # via nipype
 psutil==7.0.0
@@ -351,7 +348,6 @@ requests==2.32.4
     #   etelemetry
     #   nilearn
     #   osfclient
-    #   pooch
     #   python-gitlab
     #   requests-toolbelt
     #   templateflow
@@ -386,7 +382,7 @@ scipy==1.15.2
     #   scikit-learn
     #   sdcflows
     #   tedana
-sdcflows==2.13.1
+sdcflows==2.14.0
     # via nibabies (pyproject.toml)
 seaborn==0.13.2
     # via
@@ -402,15 +398,15 @@ six==1.17.0
     #   osfclient
     #   pybtex
     #   python-dateutil
-smriprep==0.18.0
+smriprep==0.19.1
     # via nibabies (pyproject.toml)
 sqlalchemy==2.0.41
     # via pybids
 svgutils==0.3.4
     # via niworkflows
 tedana==25.0.1
     # via nibabies (pyproject.toml)
-templateflow==24.2.2
+templateflow==25.0.3
     # via
     #   nibabies (pyproject.toml)
     #   nireports