Dear all.

I have a question concerning the estimation of cortical thickness in freesurfer. My overall goal is the comparison of a patient and matched control group with VBM and cortical thickness. My first try was the recon-all with masked MP2RAGE UNI-Images. Unfortunately it executed with error due to a not successfull skull-stripping.... Secondly I was going to skull-strip in AFNI and feed the skull-stripped image to the recon-all, but unfortunately the skull-stripping in AFNI was better but not as good as hoped.

Next idea now is using the output of the VBM8 of SPM. Is it possible to use the segmented grey matter image from SPM in the recon-all to calculate overall cortical thickness and which steps of the recon-all are needed to be excluded for that? I am basically not interested in white matter...is it needed in the algorithm in general? The step 15 starts with the wm edits. So in case I am able to use only the segmented grey matter image from the VBM toolbox to avoid needing to skull-strip, I need to start with the step 21 (autorecon2-pial) of the recon-all?

Or is there a possibility to improve the skull-stripping somehow? I tried lowering the threshold by adding the watershed trying to be more liberal, but it did not work as I was hoping...

Thank you all so much in advance! Best Regards, Laura