Thank you very much for replying so quickly! Very nice picture on your website by the way!

The probtrackx version you linked to solved the —invxfm error. I have rerun probtrackx as follows:

probtrackx2_gpu -s ${HOME}/Documents/diffusion/data.bedpostX/merged -m ${HOME}/Documents/diffusion/data.bedpostX/nodif_brain_mask -x ${HOME}/Documents/diffusion/network/masks/seed_list.txt --dir=${HOME}/Documents/diffusion/network --forcedir --network --xfm=${HOME}/Documents/diffusion/reg/str2diff.mat --seedref=${HOME}/Documents/diffusion/anat/T1w.nii.gz --invxfm=${HOME}/Documents/diffusion/reg/diff2str.mat --opd -P 5 -S 1000

I am attaching the resulting fdt_network_matrix to my email. The matrix is still all 0s except for the last column. I tried to attach a screenshot of fdt_paths.nii.gz and the masks, but they are too large. Both seem fine to me. What do you think might be the issue?

Best regards,

Ruy