Tckedit: Select fibers originating in ROI and ending in mask


Could I ask you for some help with the ROI processing options of tckedit?

  • First, I created a whole brain connectome with tck2connectome

  • Then, I extracted pathways of interest with connectome2tck. I used the AAL-atlas (containing 116 parcels) to specify the nodes. I am interested in 13 nodes of the atlas. I created one tractogram for each ROI with the following command (example for node 11): connectome2tck wholebrain_connectome.tck assignment.csv -nodes 11 -files per_node AAL Is it correct that this command selects all fibers that connect node 11 with any other node in the brain?

  • Now I would like to use the specific tractogram of node 11, overlay a binary mask and keep only those fibers that originate in node 11, enter the mask and also end within that mask. Fibers that enter the mask but then exit the mask again are supposed to be discarded.

I experimented with the options -exclude, -include, -inverse and -ends_only, however, I was not able to create my desired ROI tratcogram. Would you have any advice for me on how to solve this?

Thank you very much,