Merge pull request #224 from chrisfilo/fix/pymerge

[RTM] use nibabel to merge nifti files

fmriprep/interfaces/utils.py

@@ -105,6 +105,16 @@ def _tsv_format(translations, rot_angles, fmt='confounds'):
     return out_file
 
 
+def nii_concat(in_files):
+    from nibabel.funcs import concat_images
+    import os
+    new_nii = concat_images(in_files, check_affines=False)
+
+    new_nii.to_filename("merged.nii.gz")
+
+    return os.path.abspath("merged.nii.gz")
+
+
 def reorient(in_file):
     import os
     import nibabel as nb

fmriprep/workflows/epi.py

@@ -23,6 +23,7 @@
 
 from fmriprep.interfaces import (DerivativesDataSink, FormatHMCParam,
                                  ImageDataSink)
+from fmriprep.interfaces.utils import nii_concat
 from fmriprep.workflows.fieldmap import sdc_unwarp
 from fmriprep.viz import stripped_brain_overlay
 from fmriprep.workflows.sbref import _extract_wm
@@ -263,7 +264,9 @@ def epi_sbref_registration(settings, name='EPI_SBrefRegistration'):
     epi_split = pe.Node(fsl.Split(dimension='t'), name='EPIsplit')
     epi_xfm = pe.MapNode(fsl.preprocess.ApplyXFM(), name='EPIapplyXFM',
                          iterfield=['in_file'])
-    epi_merge = pe.Node(fsl.Merge(dimension='t'), name='EPImergeback')
+    epi_merge = pe.Node(niu.Function(input_names=["in_files"],
+                                     output_names=["merged_file"],
+                                     function=nii_concat), name='EPImergeback')
 
     ds_sbref = pe.Node(
         DerivativesDataSink(base_directory=settings['output_dir'],
@@ -356,7 +359,9 @@ def _aslist(in_value):
         ants.ApplyTransforms(), iterfield=['input_image', 'transforms'],
         name='EPIToMNITransform')
     epi_to_mni_transform.terminal_output = 'file'
-    merge = pe.Node(fsl.Merge(dimension='t'), name='MergeEPI')
+    merge = pe.Node(niu.Function(input_names=["in_files"],
+                                 output_names=["merged_file"],
+                                 function=nii_concat), name='MergeEPI')
 
     mask_merge_tfms = pe.Node(niu.Merge(2), name='MaskMergeTfms')
     mask_mni_tfm = pe.Node(