interfaces.diffusion_toolkit.postproc

SplineFilter

Link to code

Wraps command spline_filter

Smoothes TrackVis track files with a B-Spline filter.

Helps remove redundant track points and segments (thus reducing the size of the track file) and also make tracks nicely smoothed. It will NOT change the quality of the tracks or lose any original information.

Example

>>> import nipype.interfaces.diffusion_toolkit as dtk
>>> filt = dtk.SplineFilter()
>>> filt.inputs.track_file = 'tracks.trk'
>>> filt.inputs.step_length = 0.5
>>> filt.run()                                 # doctest: +SKIP

Inputs:

[Mandatory]
step_length: (a float)
        in the unit of minimum voxel size
        flag: %f, position: 1
track_file: (an existing file name)
        file containing tracks to be filtered
        flag: %s, position: 0

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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
output_file: (a file name, nipype default value: spline_tracks.trk)
        target file for smoothed tracks
        flag: %s, position: 2

Outputs:

smoothed_track_file: (an existing file name)

TrackMerge

Link to code

Wraps command track_merge

Merges several TrackVis track files into a single track file.

An id type property tag is added to each track in the newly merged file, with each unique id representing where the track was originally from. When the merged file is loaded in TrackVis, a property filter will show up in Track Property panel. Users can adjust that to distinguish and sub-group tracks by its id (origin).

Example

>>> import nipype.interfaces.diffusion_toolkit as dtk
>>> mrg = dtk.TrackMerge()
>>> mrg.inputs.track_files = ['track1.trk','track2.trk']
>>> mrg.run()                                 # doctest: +SKIP

Inputs:

[Mandatory]
track_files: (a list of items which are an existing file name)
        file containing tracks to be filtered
        flag: %s..., position: 0

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %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
output_file: (a file name, nipype default value: merged_tracks.trk)
        target file for merged tracks
        flag: %s, position: -1

Outputs:

track_file: (an existing file name)