interfaces.dipy.tracks

StreamlineTractography

Link to code

Streamline tractography using EuDX [Garyfallidis12].

[Garyfallidis12]

Garyfallidis E., “Towards an accurate brain tractography”, PhD thesis, University of Cambridge, 2012

Example

>>> from nipype.interfaces import dipy as ndp
>>> track = ndp.StreamlineTractography()
>>> track.inputs.in_file = '4d_dwi.nii'
>>> track.inputs.in_model = 'model.pklz'
>>> track.inputs.tracking_mask = 'dilated_wm_mask.nii'
>>> res = track.run() 

Inputs:

[Mandatory]
gfa_thresh: (a float, nipype default value: 0.2)
        GFA threshold to compute tracking mask
in_file: (an existing file name)
        input diffusion data
min_angle: (a float, nipype default value: 25.0)
        minimum separation angle
multiprocess: (a boolean, nipype default value: True)
        use multiprocessing
num_seeds: (an integer (int or long), nipype default value: 10000)
        desired number of tracks in tractography
peak_threshold: (a float, nipype default value: 0.5)
        threshold to consider peaks from model
save_seeds: (a boolean, nipype default value: False)
        save seeding voxels coordinates

[Optional]
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_model: (an existing file name)
        input f/d-ODF model extracted from.
in_peaks: (an existing file name)
        peaks computed from the odf
out_prefix: (a unicode string)
        output prefix for file names
seed_coord: (an existing file name)
        file containing the list of seed voxel coordinates (N,3)
seed_mask: (an existing file name)
        input mask within which perform seeding
tracking_mask: (an existing file name)
        input mask within which perform tracking

Outputs:

gfa: (a file name)
        The resulting GFA (generalized FA) computed using the peaks of the
        ODF
odf_peaks: (a file name)
        peaks computed from the odf
out_seeds: (a file name)
        file containing the (N,3) *voxel* coordinates used in seeding.
tracks: (a file name)
        TrackVis file containing extracted streamlines

TrackDensityMap

Link to code

Creates a tract density image from a TrackVis track file using functions from dipy

Example

>>> import nipype.interfaces.dipy as dipy
>>> trk2tdi = dipy.TrackDensityMap()
>>> trk2tdi.inputs.in_file = 'converted.trk'
>>> trk2tdi.run()                                   

Inputs:

[Mandatory]
in_file: (an existing file name)
        The input TrackVis track file

[Optional]
data_dims: (a list of from 3 to 3 items which are an integer (int or
         long))
        The size of the image in voxels.
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
out_filename: (a file name, nipype default value: tdi.nii)
        The output filename for the tracks in TrackVis (.trk) format
points_space: (u'rasmm' or u'voxel' or None, nipype default value:
         rasmm)
        coordinates of trk file
reference: (an existing file name)
        A reference file to define RAS coordinates space
voxel_dims: (a list of from 3 to 3 items which are a float)
        The size of each voxel in mm.

Outputs:

out_file: (an existing file name)