Dear Freesurfer experts,

I want to derive registration matrix between pcasl image and the structural space in Freesurfer (i.e. orig.mgz)

If I open orig.mgz and the pcasl image in Freesurefr I see overlap between the images (attached Figure1).

When I use "spmregister" as follow:

spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat --fsvol orig --o CBF_T1.nii

 

Then visualize "CBF_T1" using freeview I see mis-registration (attached Figure2) 

Please what I am doing wrong?

Thank you for any guidance

Jon