Fixes for adding multiple tract files to a CFF file

Author: Erik Ziegler

examples/dmri_connectivity.py

@@ -551,7 +551,7 @@ def select_aparc_annot(list_of_files):
 mapping.connect([(gpickledNetworks, CFFConverter,[("out","gpickled_networks")])])
 mapping.connect([(niftiVolumes, CFFConverter,[("out","nifti_volumes")])])
 mapping.connect([(fiberDataArrays, CFFConverter,[("out","data_files")])])
-mapping.connect([(camino2trackvis, CFFConverter,[("trackvis","tract_files")])])
+mapping.connect([(creatematrix, CFFConverter,[("filtered_tractographies","tract_files")])])
 mapping.connect([(inputnode, CFFConverter,[("subject_id","title")])])
 
 """

examples/dmri_connectivity_advanced.py

@@ -268,7 +268,7 @@
 
 probCSDstreamtrack = pe.Node(interface=mrtrix.ProbabilisticSphericallyDeconvolutedStreamlineTrack(),name='probCSDstreamtrack')
 probCSDstreamtrack.inputs.inputmodel = 'SD_PROB'
-probCSDstreamtrack.inputs.maximum_number_of_tracks = 150000
+probCSDstreamtrack.inputs.desired_number_of_tracks = 150000
 tracks2prob = pe.Node(interface=mrtrix.Tracks2Prob(),name='tracks2prob')
 tracks2prob.inputs.colour = True
 MRconvert_tracks2prob = MRconvert_fa.clone(name='MRconvert_tracks2prob')
@@ -542,7 +542,7 @@
 mapping.connect([(creatematrix, CFFConverter,[("matrix_files","gpickled_networks")])])
 mapping.connect([(niftiVolumes, CFFConverter,[("out","nifti_volumes")])])
 mapping.connect([(fiberDataArrays, CFFConverter,[("out","data_files")])])
-mapping.connect([(creatematrix, CFFConverter,[("filtered_tractography","tract_files")])])
+mapping.connect([(creatematrix, CFFConverter,[("filtered_tractographies","tract_files")])])
 mapping.connect([(inputnode, CFFConverter,[("subject_id","title")])])
 
 """

nipype/interfaces/cmtk/cmtk.py

@@ -416,6 +416,7 @@ class CreateMatrixOutputSpec(TraitedSpec):
     fiber_labels_noorphans = File(desc='Saved Numpy array with the labels for each non-orphan fiber', exists=True)
     filtered_tractography = File(desc='TrackVis file containing only those fibers originate in one and terminate in another region', exists=True)
     filtered_tractography_by_intersections = File(desc='TrackVis file containing all fibers which connect two regions', exists=True)
+    filtered_tractographies = OutputMultiPath(File(desc='TrackVis file containing only those fibers originate in one and terminate in another region', exists=True))
 
 class CreateMatrix(BaseInterface):
     """
@@ -536,6 +537,7 @@ def _list_outputs(self):
 
         _, name , _ = split_filename(self.inputs.tract_file)
         outputs['filtered_tractography'] = op.abspath(name + '_streamline_final.trk')
+        outputs['filtered_tractographies'] = [outputs['filtered_tractography'], outputs['filtered_tractography_by_intersections']]
         return outputs
 
     def _gen_outfilename(self, ext):

nipype/interfaces/cmtk/convert.py

@@ -138,7 +138,7 @@ def _run_interface(self, runtime):
         count = 0
         if isdefined(self.inputs.tract_files):
             for trk in self.inputs.tract_files:
-                trk_name = 'Tract file {cnt}'.format(cnt=count)
+                _, trk_name, _ = split_filename(trk)
                 ctrack = cf.CTrack(trk_name, trk)
                 a.add_connectome_track(ctrack)
                 count += 1

nipype/workflows/dmri/mrtrix/connectivity_mapping.py

@@ -213,7 +213,7 @@ def create_connectivity_pipeline(name="connectivity", parcellation_name='scale50
 
     probCSDstreamtrack = pe.Node(interface=mrtrix.ProbabilisticSphericallyDeconvolutedStreamlineTrack(),name='probCSDstreamtrack')
     probCSDstreamtrack.inputs.inputmodel = 'SD_PROB'
-    probCSDstreamtrack.inputs.maximum_number_of_tracks = 150000
+    probCSDstreamtrack.inputs.desired_number_of_tracks = 150000
     tracks2prob = pe.Node(interface=mrtrix.Tracks2Prob(),name='tracks2prob')
     tracks2prob.inputs.colour = True
     MRconvert_tracks2prob = MRconvert_fa.clone(name='MRconvert_tracks2prob')
@@ -479,7 +479,7 @@ def create_connectivity_pipeline(name="connectivity", parcellation_name='scale50
     mapping.connect([(creatematrix, CFFConverter,[("matrix_files","gpickled_networks")])])
     mapping.connect([(niftiVolumes, CFFConverter,[("out","nifti_volumes")])])
     mapping.connect([(fiberDataArrays, CFFConverter,[("out","data_files")])])
-    mapping.connect([(creatematrix, CFFConverter,[("filtered_tractography","tract_files")])])
+    mapping.connect([(creatematrix, CFFConverter,[("filtered_tractographies","tract_files")])])
     mapping.connect([(inputnode_within, CFFConverter,[("subject_id","title")])])
 
     """