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 # doctest: +ELLIPSIS 'tck2connectome tracks.tck aparc+aseg.nii connectome.csv' >>> mat.run() # doctest: +SKIP
- 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)
- args : a unicode 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 (int or long)
- 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.
- 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 # doctest: +ELLIPSIS 'labelconfig aparc+aseg.nii mrtrix3_labelconfig.txt parcellation.mif' >>> labels.run() # doctest: +SKIP
- 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)
- args : a unicode 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 (int or long)
- 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.
- 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() # doctest: +SKIP
- 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)
- args : a unicode 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 (int or long)
- 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.
- out_file : a pathlike object or string representing an existing file
- The output response file.