Dear FSL community,
I have been trying to generate a connectivity matrix from a volumetric Freesurfer parcellation. The command I’ve been running is:
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 --seedref=${HOME}/Documents/anat/T1w.nii.gz --xfm=${HOME}/Documents/diffusion/reg/str2diff.mat
I have run this several times with different seeds listed in seed_list.txt and consistently get an fdt_network_matrix with either all 0s or values in the order of 10^5 or 10^6 in the last column, 0s in the last row, and 0s everywhere else.
I’ve also tried passing —invxfm=${HOME}/Documents/reg/diff2str.mat to probtrackx. This causes the script to crash with a CUDA error that says it’s getting an invalid resource handle.
Do you know why these two things may be happening?
Thank you,
All the best,
Ruy
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