nipype.interfaces.mrtrix3.connectivity module¶
BuildConnectome¶
Bases: MRTrix3Base
Wrapped executable:
tck2connectome.Generate a connectome matrix from a streamlines file and a node parcellation image
Example
>>> import nipype.interfaces.mrtrix3 as mrt >>> mat = mrt.BuildConnectome() >>> mat.inputs.in_file = 'tracks.tck' >>> mat.inputs.in_parc = 'aparc+aseg.nii' >>> mat.cmdline 'tck2connectome tracks.tck aparc+aseg.nii connectome.csv' >>> mat.run()
- Mandatory Inputs:
in_file (a pathlike object or string representing an existing file) – Input tractography. Maps to a command-line argument:
%s(position: -3).out_file (a pathlike object or string representing a file) – Output file after processing. Maps to a command-line argument:
%s(position: -1). (Nipype default value:connectome.csv)- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})in_parc (a pathlike object or string representing an existing file) – Parcellation file. Maps to a command-line argument:
%s(position: -2).in_scalar (a pathlike object or string representing an existing file) – Provide the associated image for the mean_scalar metric. Maps to a command-line argument:
-image %s.in_weights (a pathlike object or string representing an existing file) – Specify a text scalar file containing the streamline weights. Maps to a command-line argument:
-tck_weights_in %s.keep_unassigned (a boolean) – By default, the program discards the information regarding those streamlines that are not successfully assigned to a node pair. Set this option to keep these values (will be the first row/column in the output matrix). Maps to a command-line argument:
-keep_unassigned.metric (‘count’ or ‘meanlength’ or ‘invlength’ or ‘invnodevolume’ or ‘mean_scalar’ or ‘invlength_invnodevolume’) – Specify the edge weight metric. Maps to a command-line argument:
-metric %s.nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument:
-nthreads %d.search_forward (a float) – Project the streamline forwards from the endpoint in search of aparcellation node voxel. Argument is the maximum traversal length in mm. Maps to a command-line argument:
-assignment_forward_search %f.search_radius (a float) – Perform a radial search from each streamline endpoint to locate the nearest node. Argument is the maximum radius in mm; if no node is found within this radius, the streamline endpoint is not assigned to any node. Maps to a command-line argument:
-assignment_radial_search %f.search_reverse (a float) – Traverse from each streamline endpoint inwards along the streamline, in search of the last node traversed by the streamline. Argument is the maximum traversal length in mm (set to 0 to allow search to continue to the streamline midpoint). Maps to a command-line argument:
-assignment_reverse_search %f.vox_lookup (a boolean) – Use a simple voxel lookup value at each streamline endpoint. Maps to a command-line argument:
-assignment_voxel_lookup.zero_diagonal (a boolean) – Set all diagonal entries in the matrix to zero (these represent streamlines that connect to the same node at both ends). Maps to a command-line argument:
-zero_diagonal.- Outputs:
out_file (a pathlike object or string representing an existing file) – The output response file.
LabelConfig¶
Bases: MRTrix3Base
Wrapped executable:
labelconfig.Re-configure parcellation to be incrementally defined.
Example
>>> import nipype.interfaces.mrtrix3 as mrt >>> labels = mrt.LabelConfig() >>> labels.inputs.in_file = 'aparc+aseg.nii' >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt' >>> labels.cmdline 'labelconfig aparc+aseg.nii mrtrix3_labelconfig.txt parcellation.mif' >>> labels.run()
- Mandatory Inputs:
in_file (a pathlike object or string representing an existing file) – Input anatomical image. Maps to a command-line argument:
%s(position: -3).out_file (a pathlike object or string representing a file) – Output file after processing. Maps to a command-line argument:
%s(position: -1). (Nipype default value:parcellation.mif)- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})in_config (a pathlike object or string representing an existing file) – Connectome configuration file. Maps to a command-line argument:
%s(position: -2).lut_aal (a pathlike object or string representing a file) – Get information from the AAL lookup table (typically “ROI_MNI_V4.txt”). Maps to a command-line argument:
-lut_aal %s.lut_basic (a pathlike object or string representing a file) – Get information from a basic lookup table consisting of index / name pairs. Maps to a command-line argument:
-lut_basic %s.lut_fs (a pathlike object or string representing a file) – Get information from a FreeSurfer lookup table(typically “FreeSurferColorLUT.txt”). Maps to a command-line argument:
-lut_freesurfer %s.lut_itksnap (a pathlike object or string representing a file) – Get information from an ITK - SNAP lookup table(this includes the IIT atlas file “LUT_GM.txt”). Maps to a command-line argument:
-lut_itksnap %s.nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument:
-nthreads %d.spine (a pathlike object or string representing a file) – Provide a manually-defined segmentation of the base of the spine where the streamlines terminate, so that this can become a node in the connection matrix. Maps to a command-line argument:
-spine %s.- Outputs:
out_file (a pathlike object or string representing an existing file) – The output response file.
LabelConvert¶
Bases: MRTrix3Base
Wrapped executable:
labelconvert.Re-configure parcellation to be incrementally defined.
Example
>>> import nipype.interfaces.mrtrix3 as mrt >>> labels = mrt.LabelConvert() >>> labels.inputs.in_file = 'aparc+aseg.nii' >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt' >>> labels.inputs.in_lut = 'FreeSurferColorLUT.txt' >>> labels.cmdline 'labelconvert aparc+aseg.nii FreeSurferColorLUT.txt mrtrix3_labelconfig.txt parcellation.mif' >>> labels.run()
- Mandatory Inputs:
in_file (a pathlike object or string representing an existing file) – Input anatomical image. Maps to a command-line argument:
%s(position: -4).in_lut (a pathlike object or string representing an existing file) – Get information from a basic lookup table consisting of index / name pairs. Maps to a command-line argument:
%s(position: -3).out_file (a pathlike object or string representing a file) – Output file after processing. Maps to a command-line argument:
%s(position: -1). (Nipype default value:parcellation.mif)- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{})in_config (a pathlike object or string representing an existing file) – Connectome configuration file. Maps to a command-line argument:
%s(position: -2).num_threads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument:
-nthreads %d.spine (a pathlike object or string representing a file) – Provide a manually-defined segmentation of the base of the spine where the streamlines terminate, so that this can become a node in the connection matrix. Maps to a command-line argument:
-spine %s.- Outputs:
out_file (a pathlike object or string representing an existing file) – The output response file.