Hi Marie,

do you have an anatomical MRI? That is what you need to give recon-all.

cheers Bruce On Wed, 30 Mar 2011, Marie ERESUE wrote:

Hi Bruce, thank you for your answer. I did recon-all with my CT and SPECT recon-all -i home/pmod/Bureau/freesurfer/subjects/... -subjid ...

and then, I tried to register CT with MNI with bbregister: bbregister --mov MNI152_T1_2mm_brainnii --s image1_CT/ --init-fsl --reg ct_recal_mni.dat --bold

But I have an error: mri/brainmask not found into CT folder, like if recon-all didn't work.

best regards,

Marie