Dear FSL team,
I have run probtrackx2 where I tested 4 seeds by 4 seeds tracking with omatrix1. The target masks are the same as the seed list. After loading the output into matlab I expected to find a matrix that's 4x4, but it's 3x3. Do you have any idea why?
Here's the command I ran:
probtrackx2 -x {path}/seeds.txt -l --xfm=bedpostX/xfms/fs2fa.mat --forcedir --opd --s bedpostX/merged -m bedpostX/nodif_brain_mask.nii.gz --os2t --s2tastext --onewaycondition --avoid={path}/ventricles.nii.gz --dir={path}/results --omatrix1 --meshspace=freesurfer --seedref={path}/fs.nii.gz --targetmasks={path}/seeds.txt
My goal is to do whole brain connectivity from 148 seeds. From my research I found that the best way is to do it through omatrix1 rather than omatrix3. Is that right?
Best regards,
Joanna
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