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