better fancier "deobliquing"

Author: chrisgorgo

fmriprep/__about__.py

@@ -105,6 +105,7 @@
     'scikit-image',
     'versioneer',
     'pyyaml',
+    'transforms3d'
 ]
 
 LINKS_REQUIRES = [

fmriprep/interfaces/images.py

@@ -21,6 +21,7 @@
     traits, TraitedSpec, BaseInterfaceInputSpec, SimpleInterface,
     File, InputMultiPath, OutputMultiPath)
 from nipype.interfaces import fsl
+from fmriprep.utils.misc import remove_rotation_and_shear
 
 LOGGER = logging.getLogger('nipype.interface')
 
@@ -293,7 +294,7 @@ def _run_interface(self, runtime):
 
 class ValidateImageInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input image')
-    deoblique = traits.Bool(False, usedefault=True)
+    remove_rotation_and_shear = traits.Bool(False, usedefault=True)
 
 
 class ValidateImageOutputSpec(TraitedSpec):
@@ -344,13 +345,6 @@ class ValidateImage(SimpleInterface):
 
     def _run_interface(self, runtime):
 
-        def deoblique(img):
-            import nibabel as nb
-            import numpy as np
-            affine = img.affine
-            affine[:3, :3] = np.diag(np.diag(affine[:3, :3]))
-            return nb.Nifti1Image(np.asanyarray(img.dataobj), affine, img.header)
-
         img = nb.load(self.inputs.in_file)
         out_report = os.path.join(runtime.cwd, 'report.html')
 
@@ -379,10 +373,10 @@ def deoblique(img):
 
         # Both match, qform valid (implicit with match), codes okay -> do nothing, empty report
         if matching_affines and qform_code > 0 and sform_code > 0:
-            if self.inputs.deoblique:
+            if self.inputs.remove_rotation_and_shear:
                 out_fname = fname_presuffix(self.inputs.in_file, suffix='_valid',
                                             newpath=runtime.cwd)
-                img = deoblique(img)
+                img = remove_rotation_and_shear(img)
                 img.to_filename(out_fname)
                 self._results['out_file'] = out_fname
             else:
@@ -435,8 +429,8 @@ def deoblique(img):
 """
         snippet = '<h3 class="elem-title">%s</h3>\n%s\n' % (warning_txt, description)
 
-        if self.inputs.deoblique:
-            img = deoblique(img)
+        if self.inputs.remove_rotation_and_shear:
+            img = remove_rotation_and_shear(img)
         # Store new file and report
         img.to_filename(out_fname)
         with open(out_report, 'w') as fobj:

fmriprep/utils/misc.py

@@ -7,17 +7,23 @@
 """
 
 
-def split_and_deoblique_func(in_file):
+def remove_rotation_and_shear(img):
+    from transforms3d.affines import decompose, compose
+    import numpy as np
+
+    T, _, Z, _ = decompose(img.affine)
+    affine = compose(T=T, R=np.diag([1, 1, 1]), Z=Z)
+    return img.__class__(np.asanyarray(img.dataobj), affine, img.header)
+
+
+def split_and_rm_rotshear_func(in_file):
     import os
     from nilearn.image import iter_img
-    import nibabel as nb
-    import numpy as np
     out_files = []
     for i, img in enumerate(iter_img(in_file)):
         out_file = os.path.abspath('vol%04d.nii.gz' % i)
-        affine = img.affine
-        affine[:3, :3] = np.diag(np.diag(affine[:3, :3]))
-        nb.Nifti1Image(np.asanyarray(img.dataobj), affine, img.header).to_filename(out_file)
+        img = remove_rotation_and_shear(img)
+        img.to_filename(out_file)
         out_files.append(out_file)
     return out_files
 

fmriprep/workflows/bold/base.py

@@ -18,7 +18,7 @@
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
 
-from fmriprep.utils.misc import split_and_deoblique_func
+from fmriprep.utils.misc import split_and_rm_rotshear_func
 from ...interfaces import (
     DerivativesDataSink,
     GiftiNameSource,
@@ -396,7 +396,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
         omp_nthreads=omp_nthreads, enhance_t2=True)
 
     # Top-level BOLD splitter
-    bold_split = pe.Node(niu.Function(function=split_and_deoblique_func, input_names=['in_file'],
+    bold_split = pe.Node(niu.Function(function=split_and_rm_rotshear_func, input_names=['in_file'],
                                       output_names=['out_files']), name='bold_split',
                          mem_gb=mem_gb['filesize'] * 3)
 

fmriprep/workflows/bold/util.py

@@ -104,7 +104,7 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, name='bold_reference_wf
     gen_ref = pe.Node(EstimateReferenceImage(), name="gen_ref",
                       mem_gb=1)  # OE: 128x128x128x50 * 64 / 8 ~ 900MB.
     # Re-run validation; no effect if no sbref; otherwise apply same validation to sbref as bold
-    validate_ref = pe.Node(ValidateImage(deoblique=True), name='validate_ref',
+    validate_ref = pe.Node(ValidateImage(remove_rotations_and_shear=True), name='validate_ref',
                            mem_gb=DEFAULT_MEMORY_MIN_GB)
     enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)