Dear all,
I'm running probtracx2 to with the aim to create the connectivity matrix, I use the following command:
probtrackx2 -x Subject_fa01_Start.nii.gz -s bedpostx/merged -m bedpostx/nodif_brain_mask -S 400 -P 5000 --steplength=0.5 --avoid=ventricles.nii --stop=Subject_fa01.nii.gz --forcedir --opd -V 2 --omatrix3 --dir=Subject_probtrackx2/ --target3=seeds.txt --cthr=0.35 --distthresh=20 --distthresh3=20
I use this command because my I only want to use as a seed the voxels with FA higher than 0.1.
After I load the the files in matlab using the script provided by Saad here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;5f3e10d9.1401
Once I have the matrix I would like to normalize it, it's correct if I divide the resulting matrix by the waytotal?
Cheers,
Manuel
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