cmtklib.interfaces.camino2trackvis module¶
Provides interfaces for functions provided by Camino-Tackvis missing in nipype or modified.
Camino2Trackvis¶
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.