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