Hello,

I am trying to put a mask that I made on the MNI brain (that had been run through recon) into individual subject space. I have already created a registration matrix using the following command:

mni152reg --s $patient --o $registration/$patient/registermni_$patient.dat --1 --save-vol

 

Now I want to apply this matrix but from MNI -> subject. So I tried doing this:

mri_vol2vol --targ $patient/mri/orig.nii --mov $mnimask/net4splitmask_bin.nii --reg $registration/$patient/registermni_$patient.dat --o $outp/$patient/net4splitmask_bin.nii --nearest --rot 180 0 0

 

But it just spits back out the MNI mask ($mnimask/net4splitmask_bin.nii) in MNI space. I tried using -inv but realized that was wrong because then it just gave me the subject’s orig. How can I get it to actually put the MNI-space mask onto the subject’s brain?

 

Sara