Wraps command camino_to_trackvis
Wraps camino_to_trackvis from Camino-Trackvis
Convert files from camino .Bfloat format to trackvis .trk format.
>>> 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()
Inputs:
[Mandatory]
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.
in_file: (an existing file name)
The input .Bfloat (camino) file.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
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.
voxel_order: (a file name)
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.
[Optional]
args: (a string)
Additional parameters to the command
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.
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_file: (an existing file name)
The input .Bfloat (camino) file.
min_length: (a float)
The minimum length of tracts to output
nifti_file: (an existing file name)
Read coordinate system from a NIfTI file.
out_file: (a file name)
The filename to which to write the .trk (trackvis) file.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
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.
voxel_order: (a file name)
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.
Outputs:
trackvis: (an existing file name)
The filename to which to write the .trk (trackvis) file.
Wraps command trackvis_to_camino
Inputs:
[Mandatory]
in_file: (an existing file name)
The input .trk (trackvis) file.
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
[Optional]
append_file: (an existing file name)
A file to which the append the .Bfloat data.
args: (a string)
Additional parameters to the command
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
in_file: (an existing file name)
The input .trk (trackvis) file.
out_file: (a file name)
The filename to which to write the .Bfloat (camino).
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal
immediately, `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
camino: (an existing file name)
The filename to which to write the .Bfloat (camino).