cmtklib.interfaces.camino2trackvis module

Provides interfaces for functions provided by Camino-Tackvis missing in nipype or modified.

Camino2Trackvis

Link to code

Bases: nipype.interfaces.base.core.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 cmtklib.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()                  
in_filea pathlike object or string representing an existing file

The input .Bfloat (camino) file. Maps to a command-line argument: -i %s (position: 1).

argsa string

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

data_dimsa 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).

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: {})

min_lengtha float

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

nifti_filea 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_filea 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).

phys_coordsa boolean

Treat the input tract points as physical coordinates (relevant for the updated camino track command). Maps to a command-line argument: --phys-coords (position: 8).

voxel_dimsa 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_ordera 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).

trackvisa pathlike object or string representing an existing file

The filename to which to write the .trk (trackvis) file.