Hi Anastasia and others,

I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command:

freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w stats/*.path.mean.txt

However, it looks like something has gone wrong with the labelling and position of the tracts (note the CST highlighted in green).

Everything was fine and correctly labelled when I checked the merged tracks.

Thanks again for your help!

Best Wishes,

Elijah

P.S. On another note, the reinit=1 trick works very well and I was able to reconstruct the tracts in almost all cases. Thanks!

Elijah Mak

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ