Hi Bhavani,

can you send us the command that you executed and the output? Frequently this means that the image orientation wasn't correct, usually because you started with a volume in analyze format. If you bring the orig.mgz up in tkmedit does it show properly (e.g. is anterior in the direction it thinks anterior it)?

cheers Bruce

On Sat, 10 Apr 2010, Bhavani shankara wrote:

Dear freesurefer experts,

I am a freesurfer beginner , e have a MPRAGE image of cortical dysplasia. Is their any way of analysing that single image and to compare with the standard (talairchie or other) template and note the involvement of the cortex.

I tried doing recon-all but in autorecon1 command itself it is stopping in the middle and saying that on comparing with the template it is not fitting with the template. Please let me know any methods

Thank you in advance expecting a answere.