I am working with a DWI dataset from the ADNI database, trying to build the connectivity matrix of a tractogram I computed from a subject with Tractoflow, using the Brainnetome Atlas and its MNI standard space. This work is for the yearly class project of my MSc.
Following a DIPY documentation tutorial (Applying image-based deformations to streamlines) for streamline registration, I tried to register my tractogram to a standard MNI space, using the deform_streamlines() function. Some streamlines seem to be incorrectly modified (I visualized the tracts) by the deformation field I computed from the b0 → MNISpace registration, but that is not the main issue as this step ran with no errors.
The problem comes when I try to generate the connectivity matrix of the mentioned tractogram (following Connectivity Matrices, ROI Intersections, and Density Maps) as it raises an error saying “Slice step cannot be zero”. While building the tractogram, I compressed the streamlines, which seems to be an important thing to mention.
How could I fix this? I can also provide code and the error traceback
Thanks for your help, I hope I am not asking a trivial thing.
Operating system and version: Linux-5.11.0-46-generic-x86_64-with-glibc2.17
Python version: Python 3.8.12 (default, Oct 12 2021, 13:49:34) [GCC 7.5.0]
dipy version: 1.4.1
H5Py: Not installed
Cvxpy: Not installed
(Working on jupyter notebook. )