nipype.interfaces.camino2trackvis.convert module¶
Provides interfaces to various commands provided by Camino-Trackvis.
Camino2Trackvis¶
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() # doctest: +SKIP
- data_dims : a list of from 3 to 3 items which are an integer (int or long)
- 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).
- args : a unicode 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).
- trackvis : a pathlike object or string representing an existing file
- The filename to which to write the .trk (trackvis) file.
Trackvis2Camino¶
Bases: CommandLine
Wrapped executable:
trackvis_to_camino.
- 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).
- 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 unicode 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).
- camino : a pathlike object or string representing an existing file
- The filename to which to write the .Bfloat (camino).