[Neuroimaging] [DIPY] track simple (not DWI) vector field data

francesco giardini giardini.fr at gmail.com
Mon Jul 15 06:45:25 EDT 2019

I'm a complete novice at the field of Dipy so, first, thank you very much
to all of you.
I would like to exploit Dipy tractography tools to draw my own data (Not
DWI), but I have some problem about the fiber directions representation.

I work with 3D images of heart muscle tissue, and I developed a simple code
that extract the fibers orientation by means of a Structure Tensor

So, I have a 3d matrix 'R' (numpy.ndarray); every R(z, y, x) element
- three eigenvalues (3x1 matrx)
- three R3 eigenvectors (3x3 matrix)
- others informations (for example, the Fractional Anisotropy, useful for
the stop criterium)

In the attached, there is a one-frame example (only one XY plane analyzed)
of the orientations maps, plotted with matplotlib and mayavi.

I'm trying to understand how to format my data to generate the streamlines.

I have reproduced some examples.
Here (
i find that csd_peaks contains the vectors informations (the source of the
tractography process?)

while here (
seems that tenfit contains the same vector field.

I'm reading also the documentation about dipy.tracking.local.LocalTracking
and dipy.tracking.local.DirectionGetter.

How I can merge my data with the Dipy structures, to generate and display
my streamlines?

I'am looking forward to your reply. Thank you very much.
Francesco Giardini

Dr. Francesco Giardini (giardini at lens.unifi.it)

LENS - European Laboratory for Non-linear Spectroscopy
Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
University of Florence - Biomedical Engineering

Tel. 055 457 2477 (off.)
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