FIX: backport niworkflows utility function

Author: mgxd

CHANGES.rst

@@ -1,3 +1,7 @@
+1.2.4 (May 4, 2020)
+===================
+Bug-fix release to ensure backwards compatibility with previous fMRIPrep versions.
+
 1.2.3 (April 16, 2020)
 ======================
 Bug-fix release enforcing BIDS-Derivatives labels on ``dseg`` file.

docs/requirements.txt

@@ -3,7 +3,7 @@ git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398
 nbsphinx
 niflow-nipype1-workflows ~= 0.0.1
 nipype>=1.3.1
-niworkflows >=1.2.0rc4,<1.4
+niworkflows ~= 1.1.12
 packaging
 pydot>=1.2.3
 pydotplus

sdcflows/interfaces/__init__.py

@@ -0,0 +1,21 @@
+# Backports
+
+
+def dseg_label(in_seg, label, newpath=None):
+    """Extract a particular label from a discrete segmentation."""
+    from pathlib import Path
+    import nibabel as nb
+    import numpy as np
+    from nipype.utils.filemanip import fname_presuffix
+
+    newpath = Path(newpath or '.')
+
+    nii = nb.load(in_seg)
+    data = np.int16(nii.dataobj) == label
+
+    out_file = fname_presuffix(in_seg, suffix='_mask',
+                               newpath=str(newpath.absolute()))
+    new = nii.__class__(data, nii.affine, nii.header)
+    new.set_data_dtype(np.uint8)
+    new.to_filename(out_file)
+    return out_file

sdcflows/workflows/outputs.py

@@ -41,9 +41,9 @@ def init_sdc_unwarp_report_wf(name='sdc_unwarp_report_wf', forcedsyn=False):
         Affine transform from T1 space to BOLD space (ITK format)
 
     """
+    from ..interfaces import dseg_label as _dseg_label
     from niworkflows.interfaces import SimpleBeforeAfter
     from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
-    from niworkflows.utils.images import dseg_label as _dseg_label
 
     DEFAULT_MEMORY_MIN_GB = 0.01
 
@@ -58,7 +58,10 @@ def init_sdc_unwarp_report_wf(name='sdc_unwarp_report_wf', forcedsyn=False):
 
     sel_wm = pe.Node(niu.Function(function=_dseg_label), name='sel_wm',
                      mem_gb=DEFAULT_MEMORY_MIN_GB)
-    sel_wm.inputs.label = 2
+    # API CHANGE: sMRIPrep 0.6.x
+    # https://github.com/poldracklab/smriprep/issues/176
+    # https://github.com/poldracklab/smriprep/pull/177 changes this to 2
+    sel_wm.inputs.label = 3
 
     bold_rpt = pe.Node(SimpleBeforeAfter(), name='bold_rpt',
                        mem_gb=0.1)

setup.cfg

@@ -29,7 +29,7 @@ install_requires =
     nibabel >=3.0.1
     niflow-nipype1-workflows ~= 0.0.1
     nipype >=1.3.1,<2.0
-    niworkflows >=1.2.0rc4,<1.4
+    niworkflows ~= 1.1.12
     numpy
     pybids >= 0.9.2
     templateflow >=0.4