nipype.interfaces.mrtrix3.connectivity module

BuildConnectome

Link to code

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()
in_filea pathlike object or string representing an existing file

Input tractography. Maps to a command-line argument: %s (position: -3).

out_filea 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)

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

environa 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_parca pathlike object or string representing an existing file

Parcellation file. Maps to a command-line argument: %s (position: -2).

in_scalara 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_weightsa 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_unassigneda 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.

nthreadsan integer

Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

search_forwarda 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_radiusa 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_reversea 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_lookupa boolean

Use a simple voxel lookup value at each streamline endpoint. Maps to a command-line argument: -assignment_voxel_lookup.

zero_diagonala 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_filea pathlike object or string representing an existing file

The output response file.

LabelConfig

Link to code

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()
in_filea pathlike object or string representing an existing file

Input anatomical image. Maps to a command-line argument: %s (position: -3).

out_filea 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)

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

environa 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_configa pathlike object or string representing an existing file

Connectome configuration file. Maps to a command-line argument: %s (position: -2).

lut_aala 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_basica 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_fsa 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_itksnapa 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.

nthreadsan integer

Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

spinea 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_filea pathlike object or string representing an existing file

The output response file.

LabelConvert

Link to code

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()
in_filea pathlike object or string representing an existing file

Input anatomical image. Maps to a command-line argument: %s (position: -4).

in_luta 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_filea 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)

argsa string

Additional parameters to the command. Maps to a command-line argument: %s.

environa 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_configa pathlike object or string representing an existing file

Connectome configuration file. Maps to a command-line argument: %s (position: -2).

num_threadsan integer

Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

spinea 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_filea pathlike object or string representing an existing file

The output response file.