Dear FSL experts,

I have drawn a mask in the precuneus cortex in MNI 2mm resolution space. The ROI appared good, located just where I wanted.

Then I registered MNI space to my higher individual anatomical image (EPI space) and it worked perfectly.

Then I registered my precuneus.nii.gz (ROI) from MNI space to highres anatomical space.

The problem comes when I open my MNI.to.highres image and load the precuneus.to.highres image in fslview...my roi appears moved to the brain stem!!!!

The commands I used to make the different steps were:

flirt -in MNI152_T1_2mm_brain -ref highres -omat MNI.to.highres.mat -out MNI.to.t1.nii.gz
flirt -in highres -ref precuneus -omat precuneus.to.highres.mat -out precuneus.to.highres.nii.gz –applyxfm

Any idea of what can be happening and how to fix this?

Best regards,

Rosalia.