To whom it may concern.
We've been working with Freesurfer, under Prof. Ming Hsu at the University of Illinois at Urbana Champaign.
We ran the group analysis tutorial using the provided buckner_data, but when we displayed our results visually, there were numerous discrepancies with the images provided in the visualization tutorial. Our instructor told us to rerun the precprocessing steps (recon-all) on all of the subjects in the group_analysis_tutorial data. However, these subjects lack .mgz or image files, so we can't rerun the preprocessing stream. We sent the following email to our instructor and were told to email the freesurfer mailing list. What can we do or where can we find help?
Thank you for your time!
Mukta Vaidya Luke Tseng
Sent email:
Prof. Hsu,
We tried using the -no-isrunning flag, and recieved basically the same error. Then we went into the one of the subjects folders and tried to find the initial mgz or image files needed to start the entire process and could not find any (we checked in all of the subfolders). We think the problem is that no image files are present in any of the subject folders in the group analysis tutorial, which would mean that we can't "reprocess" the data using recon-all. Only the resulting files produced after preprocessing were present in the subject folder we looked at (004).
Just to check if this was the case, we tried running recon-all using the same flag on another subject in the Buckner data, bert. This also exited with an error, but not with the same error. What do we do now?
Mukta & Luke