Hi Sara,
the base (subject template) is pretty robust. Not sure what goes on that it fails on 50% of your images. You should debug to see why it fails?
- look at the input images, e.g. the norm.mgz from both your time points from the cross sectional processing
- check the log file for the base run to see where it stops.
- also check the norm.mgz in the base, is it blurry or 2 ghosts? That could mean that the registration fails?
- search the log file for the mri_robust_template command (the registration) and see if that fails
On top of that, even if you get it to work, any changes you quantify between your two time points could be purely caused by the scanner change. Or are you trying to quantify scanner effects?
Best, Martin
Am 18.01.2018 um 11:32 schrieb Ambrosino di Bruttopilo-3, S.:
Dear experts,
I run FreeSurfer 6.0 longitudinal pipeline on a set of scans acquired with identical protocol (ADNI) but 2 different Philips 3T scanners (all time 1 with Achieva, all time 2 with Ingenia). Unfortunately ~ 50% of the within-subjects templates completely failed. Is there anything I could try to fix this, or should just accept that is not possible to run FS longitudinal with this data?
Thanks a lot!
Sara
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