Hi Laura,

this should not happen. Probably something got mixed up (e.g. creating a template from 2 time points that are from different subjects could cause these problems). For testing, you could select one subject from the middle of your data set , copy the 2 cross sectionally processed time points into a new directory and create the base for this subject there.

Best, Martin

On 04/02/2014 09:10 AM, L. Koenders wrote:

Dear FreeSurfer people,

I have a question regarding the longitudinal pipeline, because something goes very wrong with my output.

A short summary of my project: I have 3Tesla data from two timepoints, consisting of 50 people, so 100 scans in total. I have two groups, a control and an experimental group (cannabis users).

In FS v5.3.0, I ran all scans through the Cross pipeline, and made brainmask.mgz pial edits where necessary. So far so good. Subsequently, I ran all the scans (all the edited scans) through the Base pipeline. This is when I ran into troubles, because only 2 templates (out of the whole group) turned out all right. The surfaces of all other scans are skipping gyri (for an example see attachment template_surfs). The scans that turned out allright were the very first and very last one of my subjects, which i find suspicous.

I could of course try editing all the templates using control points, however I have this feeling that something else is going wrong with the registration of baseline and follow up scan. Do you know if this is a common error, and if I can do anything to fix it?

I hope you can help me!

Thanks & best regards, Laura Koenders

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