Tracks displaced

[Marc Ramos]

Hi everyone!

I was tracking a DTI with mrtrix pipeline of connectome mapper and found that the converted.trk file looked like this. In the end of the pipeline, there are a lot of errors:

An index error occured for fiber 1199939. This means that the fiber start or endpoint is outside the volume. Continue.
An index error occured for fiber 1199945. This means that the fiber start or endpoint is outside the volume. Continue.
An index error occured for fiber 1199946. This means that the fiber start or endpoint is outside the volume. Continue.
An index error occured for fiber 1199951. This means that the fiber start or endpoint is outside the volume. Continue.

Like these ones. My hypothesis is that something weird happened in the MRTrix2TrackVis function, that passes the wm_resampled image as reference (I guess it applies the affine of the image)
I have tested the convertion via other methods but the result is never good, always a displacement or rotation of some kind...
The streamline_final.trk looks cut in the upper part, like the fibers that go beyond the mask got cropped.
Any idea of what's going on?

Thanks in advance.
Marc.

[Liang Cao]

I have the same problem. Have you solved it?