Hi
I am trying to do tractography from a seed voxel to the
hipocampus.
I run the command as so:
probtrackx -s merged -m nodif_brain_mask -x my_seed-coords.txt
--mode=simple --seedref=/usr/local/fsl/etc/standard/avg152T1
--xfm=xfms/standard2diff.mat --opd -o my_outfile
--targetmasks=my_target-mask.txt
and my_target-mask.txt containes two mask-file names:
right_HC_mask.nii
left_HC_mask.nii
I have two questions:
1) Is this the correct way of running this command?
2) The masks are averge volumes in MNI space. do I need to do a
transformation to bring target-masks to diff-space of each
subject, or will that be done automatically?
Many thanks.
Naj
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