interfaces.camino2trackvis.convert¶
Camino2Trackvis¶
Wraps the executable command 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
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
The input .Bfloat (camino) file.
argument: ``-i %s``, position: 1
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.
argument: ``-d %s``, position: 4
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.
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.
argument: ``--voxel-order %s``, position: 6
[Optional]
out_file: (a pathlike object or string representing a file)
The filename to which to write the .trk (trackvis) file.
argument: ``-o %s``, position: 2
min_length: (a float)
The minimum length of tracts to output
argument: ``-l %d``, position: 3
nifti_file: (a pathlike object or string representing an existing
file)
Read coordinate system from a NIfTI file.
argument: ``--nifti %s``, position: 7
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
trackvis: (a pathlike object or string representing an existing file)
The filename to which to write the .trk (trackvis) file.
Trackvis2Camino¶
Wraps the executable command trackvis_to_camino
.
Inputs:
[Mandatory]
in_file: (a pathlike object or string representing an existing file)
The input .trk (trackvis) file.
argument: ``-i %s``, position: 1
[Optional]
out_file: (a pathlike object or string representing a file)
The filename to which to write the .Bfloat (camino).
argument: ``-o %s``, position: 2
append_file: (a pathlike object or string representing an existing
file)
A file to which the append the .Bfloat data.
argument: ``-a %s``, position: 2
args: (a unicode string)
Additional parameters to the command
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', nipype default value: {})
Environment variables
Outputs:
camino: (a pathlike object or string representing an existing file)
The filename to which to write the .Bfloat (camino).