Freesurfer ROIs for track editing


#1

Hello MRTrix community,

I did a whole brain tractography and now I want to just have specific tracts. I know how to edit tracts based on spherical ROI. But is there any way to give the freesurfer parcellation regions as the ROI based on their names or IDs in the LUT? If no, what is the best way for introducing a specific ROI based on freesurfer parcellation file?


#2

Im still new to mrtrix and working through it myself but it sounds like you want connectome2tck. You will need to specify in the previous step generating a connectome from streamlines that you want to output the node assignments for the streamlines

http://mrtrix.readthedocs.io/en/latest/reference/commands/connectome2tck.html


#3

Thank you Nialljb. Actually this is also a good solution. But it doesn’t work when you want to do seeding in a specific region. I found a way to extract each specific region as a mask from freesurfer parcellation file. I did the tractography and it worked well. However by choosing a region as the seeding region, and another region as an included region and by using -stop property I expect that only tracts who start from the first region and terminates in the second region be shown. But I am seeing also other tracts who terminates in the GMWM border. If you have any idea about this problem I would appreciate if you help me.


Tracts out of included regions
#4

Not sure, but maybe what’s missing is the -seed_unidirectional option…?