def _run_interface(self, runtime):
if isdefined(self.inputs.additional_maps):
additional_maps = dict( (split_filename(add_map)[1],add_map) for add_map in self.inputs.additional_maps if add_map != '')
else:
additional_maps = {}
if self.inputs.probtrackx:
probtrackx_cmat(voxel_connectivity_files = self.inputs.track_file, roi_volumes=self.inputs.roi_volumes,
parcellation_scheme=self.inputs.parcellation_scheme, atlas_info=self.inputs.atlas_info,
output_types = self.inputs.output_types)
elif len(self.inputs.track_file) > 1:
prob_cmat(intrk=self.inputs.track_file, roi_volumes=self.inputs.roi_volumes,
parcellation_scheme=self.inputs.parcellation_scheme,atlas_info = self.inputs.atlas_info,
output_types=self.inputs.output_types)
else:
cmat(intrk=self.inputs.track_file[0], roi_volumes=self.inputs.roi_volumes,
parcellation_scheme=self.inputs.parcellation_scheme,atlas_info = self.inputs.atlas_info,
compute_curvature=self.inputs.compute_curvature,
additional_maps=additional_maps,output_types=self.inputs.output_types)
if 'cff' in self.inputs.output_types:
cvt = cmtk.CFFConverter()
cvt.inputs.title = 'Connectome mapper'
cvt.inputs.nifti_volumes = self.inputs.roi_volumes
cvt.inputs.tract_files = ['streamline_final.trk']
cvt.inputs.gpickled_networks = glob.glob(os.path.abspath("connectome_*.gpickle"))
cvt.run()
return runtime
def _run_interface(self, runtime):
if isdefined(self.inputs.additional_maps):
additional_maps = dict((split_filename(add_map)[1], add_map)
for add_map in self.inputs.additional_maps
if add_map != '')
else:
additional_maps = {}
if self.inputs.probtrackx:
probtrackx_cmat(
voxel_connectivity_files=self.inputs.track_file,
roi_volumes=self.inputs.roi_volumes,
parcellation_scheme=self.inputs.parcellation_scheme,
atlas_info=self.inputs.atlas_info,
output_types=self.inputs.output_types)
elif len(self.inputs.track_file) > 1:
prob_cmat(intrk=self.inputs.track_file,
roi_volumes=self.inputs.roi_volumes,
parcellation_scheme=self.inputs.parcellation_scheme,
atlas_info=self.inputs.atlas_info,
output_types=self.inputs.output_types)
else:
cmat(intrk=self.inputs.track_file[0],
roi_volumes=self.inputs.roi_volumes,
parcellation_scheme=self.inputs.parcellation_scheme,
atlas_info=self.inputs.atlas_info,
compute_curvature=self.inputs.compute_curvature,
additional_maps=additional_maps,
output_types=self.inputs.output_types)
if 'cff' in self.inputs.output_types:
cvt = cmtk.CFFConverter()
cvt.inputs.title = 'Connectome mapper'
cvt.inputs.nifti_volumes = self.inputs.roi_volumes
cvt.inputs.tract_files = ['streamline_final.trk']
cvt.inputs.gpickled_networks = glob.glob(
os.path.abspath("connectome_*.gpickle"))
cvt.run()
return runtime
def build_matrix(self):
#make sure you output into cmp's connectome folder
prevdir=os.getcwd()
os.chdir(self.sub_dir + '/NIPYPE/diffusion_pipeline/connectome_stage/compute_matrice')
#only prob_cmat has been successfully tested as of 12.18.2015
#cmat takes extra arguments compute_curvature and additional_maps
#hard to say if probtrackx will work; if it doesn't, the issue's probably in generate_tracklist
if self.probtrackx:
probtrackx_cmat(voxel_connectivity_files = self.track_file, roi_volumes=self.roi_volumes,
parcellation_scheme=self.parcellation_scheme, atlas_info=self.atlas_info,
output_types = self.output_types)
elif len(self.track_file) > 1:
prob_cmat(intrk=self.track_file, roi_volumes=self.roi_volumes,
parcellation_scheme=self.parcellation_scheme,atlas_info = self.atlas_info,
output_types=self.output_types)
else:
additional_maps = {}
cmat(intrk=self.track_file[0], roi_volumes=self.roi_volumes,
parcellation_scheme=self.parcellation_scheme,atlas_info = self.atlas_info,
compute_curvature=self.compute_curvature,
additional_maps=additional_maps,output_types=self.output_types)
os.chdir(prevdir)