Good afternoon,

I'm trying to find a solution for this for a while, so I would really appreciate your help on this one.

Is it possible to create a landmark (ROI sphere mask) and create a label with this (like 'Landmark1') in FSL? After transforming the landmarks from standard brain to subject brain using SPM normalise, the order of the cluster indices (using the FSL cluster command) varies per subject. However, I need the same order of landmarks for each subject for my geometric morphometics analysis. If I could include a label, and this sticks to the landmark after the SPM normalise transformation, this problem might be solved. I would like to hear your suggestions.

If this isn't possible, would it be an idea to create one mask file with 163 landmarks (ROI spheres) of which each sphere has a different intensity (landmark 1 fslmaths -mul 1000, landmark 2 -mul2000 etc) and run a bash script to define each landmark? I had troubles merging the different intensity masks as the intensity will become 1 when I merge the different landmark files(=sphere masks) in one file. Do you perhaps have some suggestions on how to keep the differences in intensity when I merge all the masks?

Your help is much appreciated(!).

Kind regards,

Liza