Hi Guang,

has anyone ever answered to your question? Probably it was missed.

It is very strange that the longitudinals fail when the base and the cross sectionals worked! Also the brainmask step in the -long run simply maps the brainmask from the base to the current time point. It cannot fail.

Something else is going on. Maybe your not calling the longitudinal correctly. Also you cannot change the watershed as there is no skull stripping done.

Maybe you got it working, if not, I'd need to know - your FS version - the commands you used - the log file

Cheers, Martin

On Mon, 2010-03-01 at 10:13 -0600, Guang Zeng wrote:

Hi, there,

I have a question about FS longitudinal stream,

I have data from two time points which have been processed by FreeSurfer cross-sectional stream. I also built the base template using recon-all -base command, everything looks fine.

When I ran the longitudinal stream, one of them stopped at the first step, it failed to do the skull stripping. I changed the watershed threshold, it works now.

The question is, for this time point data, I want to use the following command line to finish the rest longitudinal analysis,

recon-all -long tp_dat1 base_id -autorecon2 -autorecon3

Is it correct?

Thanks! Guang

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