Hi Saad
Just a quick question about the NxN connectivity matrix of probtrackx2. I have tried omatrix3, and it seems that I also have to put target3 in the command line.
So my command is something like this
probtrackx2
-x ....../${roi}.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 50
--xfm=....../$1/bedpostX/xfms/standard2ptx.mat --forcedir --opd
-s ....../$1/bedpostX/merged
-m ....../$1/bedpostX/nodif_brain_mask
--dir=....../$1/pt2/track_${roi}
--targetmasks=....../clf_masks/all_GM2.txt --os2t
--omatrix3 --target3=....../clf_masks/all_GM2.txt;
(my ROIs are '01', '02', etc. )
And it returned the file 'fdt_matrix3.odt' in each result folder (e.g., 'track_01', track_02' etc.). This fdt_matrix3 however did not look like a NxN matrix that I expected.
Did I miss anything here? Thanks in advance -Chiashu
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