Merge pull request #206 from chrisfilo/enh/reorient

[RTM] use nibabel to reorient to avoid unecessary interpolation

fmriprep/interfaces/utils.py

@@ -104,3 +104,12 @@ def _tsv_format(translations, rot_angles, fmt='confounds'):
 
     return out_file
 
+
+def reorient(in_file):
+    import os
+    import nibabel as nb
+
+    _, outfile = os.path.split(in_file)
+    nii = nb.as_closest_canonical(nb.load(in_file))
+    nii.to_filename(outfile)
+    return os.path.abspath(outfile)

fmriprep/workflows/anatomical.py

@@ -11,7 +11,6 @@
 import os.path as op
 
 from nipype.interfaces import ants
-from nipype.interfaces import freesurfer as fs
 from nipype.interfaces import fsl
 from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
@@ -25,6 +24,7 @@
 
 from fmriprep.interfaces import (DerivativesDataSink, IntraModalMerge,
                                  ImageDataSink)
+from fmriprep.interfaces.utils import reorient
 from fmriprep.viz import stripped_brain_overlay
 
 
@@ -47,7 +47,9 @@ def t1w_preprocessing(name='t1w_preprocessing', settings=None):
     t1wmrg = pe.Node(IntraModalMerge(), name='MergeT1s')
 
     # 1. Reorient T1
-    arw = pe.Node(fs.MRIConvert(out_type='niigz', out_orientation='LAS'),
+    arw = pe.Node(niu.Function(input_names=['in_file'],
+                               output_names=['out_file'],
+                               function=reorient),
                   name='Reorient')
 
     # 2. T1 Bias Field Correction

fmriprep/workflows/sbref.py

@@ -16,12 +16,12 @@
 from nipype.interfaces import io as nio
 from nipype.interfaces import utility as niu
 from nipype.interfaces import fsl, c3
-from nipype.interfaces import freesurfer as fs
 from nipype.interfaces import ants
 from niworkflows.interfaces.masks import BETRPT
 from niworkflows.interfaces.registration import FLIRTRPT
 
 from fmriprep.utils.misc import _first, gen_list
+from fmriprep.interfaces.utils import reorient
 from fmriprep.interfaces import (ReadSidecarJSON, IntraModalMerge,
                                  DerivativesDataSink, ImageDataSink)
 from fmriprep.workflows.fieldmap import sdc_unwarp
@@ -135,10 +135,10 @@ def sbref_t1_registration(name='SBrefSpatialNormalization', settings=None):
     )
 
     # Make sure sbref is in RAS coordinates
-    reorient = pe.Node(
-        fs.MRIConvert(out_type='niigz', out_orientation='RAS'),
-        name='SBRefReorient'
-    )
+    to_ras = pe.Node(niu.Function(input_names=['in_file'],
+                                  output_names=['out_file'],
+                                  function=reorient),
+                     name='SBRefReorient')
 
     # Extract wm mask from segmentation
     wm_mask = pe.Node(
@@ -159,12 +159,12 @@ def sbref_t1_registration(name='SBrefSpatialNormalization', settings=None):
     invt_bbr = pe.Node(fsl.ConvertXFM(invert_xfm=True), name="Flirt_BBR_Inv")
 
     workflow.connect([
-        (inputnode, reorient, [('sbref_brain', 'in_file')]),
+        (inputnode, to_ras, [('sbref_brain', 'in_file')]),
         (inputnode, wm_mask, [('t1_seg', 'in_file')]),
         (inputnode, flt_bbr_init, [('t1_brain', 'reference')]),
         (inputnode, flt_bbr, [('t1_brain', 'reference')]),
-        (reorient, flt_bbr_init, [('out_file', 'in_file')]),
-        (reorient, flt_bbr, [('out_file', 'in_file')]),
+        (to_ras, flt_bbr_init, [('out_file', 'in_file')]),
+        (to_ras, flt_bbr, [('out_file', 'in_file')]),
         (flt_bbr_init, flt_bbr, [('out_matrix_file', 'in_matrix_file')]),
         (wm_mask, flt_bbr, [('out_file', 'wm_seg')]),
         (flt_bbr, invt_bbr, [('out_matrix_file', 'in_file')]),