interfaces.mrtrix3.connectivity

BuildConnectome

Link to code

Wraps command 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()                                 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input tractography
        flag: %s, position: -3
out_file: (a file name, nipype default value: connectome.csv)
        output file after processing
        flag: %s, position: -1

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_parc: (an existing file name)
        parcellation file
        flag: %s, position: -2
in_scalar: (an existing file name)
        provide the associated image for the mean_scalar metric
        flag: -image %s
in_weights: (an existing file name)
        specify a text scalar file containing the streamline weights
        flag: -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)
        flag: -keep_unassigned
metric: (u'count' or u'meanlength' or u'invlength' or
         u'invnodevolume' or u'mean_scalar' or u'invlength_invnodevolume')
        specify the edge weight metric
        flag: -metric %s
nthreads: (an integer (int or long))
        number of threads. if zero, the number of available cpus will be
        used
        flag: -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.
        flag: -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.
        flag: -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).
        flag: -assignment_reverse_search %f
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
vox_lookup: (a boolean)
        use a simple voxel lookup value at each streamline endpoint
        flag: -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)
        flag: -zero_diagonal

Outputs:

out_file: (an existing file name)
        the output response file

LabelConfig

Link to code

Wraps command 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()                                 

Inputs:

[Mandatory]
in_file: (an existing file name)
        input anatomical image
        flag: %s, position: -3
out_file: (a file name, nipype default value: parcellation.mif)
        output file after processing
        flag: %s, position: -1

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
in_config: (an existing file name)
        connectome configuration file
        flag: %s, position: -2
lut_aal: (a file name)
        get information from the AAL lookup table (typically
        "ROI_MNI_V4.txt")
        flag: -lut_aal %s
lut_basic: (a file name)
        get information from a basic lookup table consisting of index / name
        pairs
        flag: -lut_basic %s
lut_fs: (a file name)
        get information from a FreeSurfer lookup table(typically
        "FreeSurferColorLUT.txt")
        flag: -lut_freesurfer %s
lut_itksnap: (a file name)
        get information from an ITK - SNAP lookup table(this includes the
        IIT atlas file "LUT_GM.txt")
        flag: -lut_itksnap %s
nthreads: (an integer (int or long))
        number of threads. if zero, the number of available cpus will be
        used
        flag: -nthreads %d
spine: (a file name)
        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.
        flag: -spine %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_file: (an existing file name)
        the output response file