Hi xuan,

You can try freesurfer 5.3 for the base creation and see if that fixes it. If not, send me the two norm.mgz of the cross time points and I take a look.

Thanks, martin

Sent via my smartphone, please excuse brevity.

-------- Original message -------- From: XUAN AMELIA TRAN tranx@ucla.edu Date:07/04/2014 4:00 AM (GMT+01:00) To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Base Misalignment during Longitudinal Image Processing

Hi there,

I used inputs from two time points that have been processed with Freesurfer 5.0.0 cross-sectional pipeline.

I used the following command to create the base template (using Freesurfer 5.0.0):

recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all

The job log said the run was successful. However when inspected with freeview, the norm.mgz for base output shows misalignment (see image attached).

Does anyone know how to fix this problem?

Thank you!

Xuan