nipype.interfaces.camino2trackvis.convert module

Provides interfaces to various commands provided by Camino-Trackvis.

Camino2Trackvis

Link to code

Bases: CommandLine

Wrapped executable: camino_to_trackvis.

Wraps camino_to_trackvis from Camino-Trackvis

Convert files from camino .Bfloat format to trackvis .trk format.

Example

>>> import nipype.interfaces.camino2trackvis as cam2trk
>>> c2t = cam2trk.Camino2Trackvis()
>>> c2t.inputs.in_file = 'data.Bfloat'
>>> c2t.inputs.out_file = 'streamlines.trk'
>>> c2t.inputs.min_length = 30
>>> c2t.inputs.data_dims = [128, 104, 64]
>>> c2t.inputs.voxel_dims = [2.0, 2.0, 2.0]
>>> c2t.inputs.voxel_order = 'LAS'
>>> c2t.run()
Mandatory Inputs:

  • data_dims (a list of from 3 to 3 items which are an integer) – Three comma-separated integers giving the number of voxels along each dimension of the source scans. Maps to a command-line argument: -d %s (position: 4).

  • in_file (a pathlike object or string representing an existing file) – The input .Bfloat (camino) file. Maps to a command-line argument: -i %s (position: 1).

  • voxel_dims (a list of from 3 to 3 items which are a float) – Three comma-separated numbers giving the size of each voxel in mm. Maps to a command-line argument: -x %s (position: 5).

  • voxel_order (a pathlike object or string representing a file) – Set the order in which various directions were stored. Specify with three letters consisting of one each from the pairs LR, AP, and SI. These stand for Left-Right, Anterior-Posterior, and Superior-Inferior. Whichever is specified in each position will be the direction of increasing order. Read coordinate system from a NIfTI file. Maps to a command-line argument: --voxel-order %s (position: 6).

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: {})

  • min_length (a float) – The minimum length of tracts to output. Maps to a command-line argument: -l %d (position: 3).

  • nifti_file (a pathlike object or string representing an existing file) – Read coordinate system from a NIfTI file. Maps to a command-line argument: --nifti %s (position: 7).

  • out_file (a pathlike object or string representing a file) – The filename to which to write the .trk (trackvis) file. Maps to a command-line argument: -o %s (position: 2).

Outputs:

trackvis (a pathlike object or string representing an existing file) – The filename to which to write the .trk (trackvis) file.

Trackvis2Camino

Link to code

Bases: CommandLine

Wrapped executable: trackvis_to_camino.

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – The input .trk (trackvis) file. Maps to a command-line argument: -i %s (position: 1).

Optional Inputs:

  • append_file (a pathlike object or string representing an existing file) – A file to which the append the .Bfloat data. . Maps to a command-line argument: -a %s (position: 2).

  • 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: {})

  • out_file (a pathlike object or string representing a file) – The filename to which to write the .Bfloat (camino). Maps to a command-line argument: -o %s (position: 2).

Outputs:

camino (a pathlike object or string representing an existing file) – The filename to which to write the .Bfloat (camino).