rel: 25.2.0

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