Hi Laouchedi

these alignments look fine. I am a bit concerned at how dark your images are near the top of the head. What coil are you using? This is probably why you are having trouble.

cheers Bruce On Tue, 28 May 2013, LAOUCHEDI MAKHLOUF wrote:

Hi     i have a problem when running "recon-all -all", so i decided to split the process into three staps : "recon-all -autorecon1", ""recon-all -autorecon2" and "recon-all -autorecon3". i have just finished with the first step (recon-all -autorecon1) and looked for misalignment in talairach transform for all subjects using "tkregister2 --mgz --s ctr1 --fstal"  (i can't use "--surf orig " because i haven't the surfaces yet). so i used the small red cross in the coronal, sagittal and axial views to align as much as possible. my goal is to extract the cortical labels (cortical parcellation). is it necessary to have a precise talairach transform just for this purpose ?

Thank you