Dear FSL experts,
I am trying to run probtrackx2 from the command line with the --network and --omatrix1 option to obtain seed-to-seed connectivity.
This is my command:
probtrackx2 --network --seed=${subrois}/${sub}_Listofseeds.txt --omatrix1 --samples=${subdir}/merged --mask=${subdir}/nodif_brain_mask --nsamples 50 --pd --forcedir --dir=${outdir}/${sub}
where ${sub}_Listofseeds.txt is a txt file containing the path/to/seeds.nii.gz (each on a new line)
However, I get the following error message:
/Users/sbaldi/Desktop/WORK_DATA/OCD/ROIs_warped/Sub005/Sub005_Listofseeds.txt: is an unrecognised token!
try: probtrackx2 --help
I however do not understand where my error stands.
Any suggestions?
Thanks in advance,
Sam
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