Hi Freesurfer help,
I am currently going through the workflow following the recommended reconstruction for 4 of my new subjects. I used recon-all scripts fo the stages 1 and 2. Now I am checking if the surfaces are correct with tkmedit. I have found a strange behavior with this viewer. When I run:
tkmedit 010748_8 wm.mgz rh.white -aux brainmask.mgz -aux-surface lh.white,
It then show the coronal slice 128 and some surfaces are badly position (see attached image bad_slice_128.tif) with zigzag like surfaces. The funny part is that I then surf through the volume, and some images are bad and some a perfect. Then I go back to the coronal slice 128 (see attached image good_slice_128.tif), and the surfaces are then perfect. And after that all the surfaces in the volume are position correctly. He is the summary of my error report:
Machine: lacolombiana (in the martinos center) version: source /usr/local/freesurfer/nmr-std-env SUBJECT_DIR /autofs/space/rao_001/users/patrickp/propofol/ which tkmedit: /usr/local/freesurfer/stable/bin//tkmedit Current working directory: /autofs/space/rao_001/users/patrickp/propofol/010748_8 Subject: 010748_8
This same thing happen with my other 3 subjects: 010748_10, 010748_11, 010748_112. Then I run tkmedit in machine rao, and the funny behavior disappeared. Is there anything that you guys can think of that I must modify in my machine to fix this?
Thanks,
--Camilo
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