Hi Elena,
FreeSurfer put inputs in RAS coordinates (during the conform step at the very beginning), so it will take care of this. But only if the correct information is available from the input image header. If that header was corrupted earlier, it is impossilbe to know what coordinates the input is in and then this can happen.
One thing you can try is to open the orig.mgz from both time points in freeview. Are they in the same orientation? If so , there might be a different problem. If not, you should go back to the original scans (dicom) and convert them to nifti directly (if possible) using mri_convert.
Best, Martin
On Fri, 2018-12-07 at 11:32 +1100, Elena Pozzi wrote:
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Dear FreeSurfer Experts,
I have some baseline and follow-up MRI scans that I would like to process through the longitudinal stream.
Some of the baseline images were originally in Analyze format (LAS orientation) and were converted into nifti (keeping the LAS orientation) and then processed through the recon-all stream (and edited). A few other baseline images were instead in nifti format (RAS orientation). The follow-up images were all in nifti format (RAS orientation) and were as well processed through the recon-all stream and edited.
For all the images that were originally in Analyze format at baseline and converted in nifti, the within subject template (base) failed, i.e., the surfaces clearly do not properly follow the WM and GM boundaries. Instead, for the baseline images that were in nifti format the template looks fine.
Given that the problem arose only with the Analyze images, could the different orientation (LAS and RAS) explain the issue? If so, is it possible to flip the orientation after the preprocessing, keeping the edits that were made on the pial of the baseline images?
Apologies if any of these questions was already asked but I couldn’t find an answer.
Thank you very much,
Elena
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