Hi,
The two mri/orig/xxx.mgz files load in tkmedit with the orientations correctly assigned.
When I load rawavg.mgz, I get the following message (which seems relevant), and then it loads with the coronal and sagittal orientations swapped.
% [catherine:phelpslab/Cate/extinction] cate% tkmedit AS083182 rawavg.mgz ----------------------------------------------------------------- Could not find the direction cosine information. Will use the CORONAL orientation. If not suitable, please provide the information in /Volumes/phelpslab/Cate/extinction//AS083182/mri/rawavg.mgz.
Thanks, Cate
are the mri/orig/XXX.mgz files ok? What about the mri/rawavg.mgz?
Catherine Hartley wrote:
Hi,
I just ran autorecon1 on a batch of data and when I view the brainmask in tkmedit, selecting the coronal orientation actually displays the sagittal orienation and vice versa (horizontal is fine). Also, when I check the talairach using tkregister, the talairach comparison volume comes up with a strange diagonal orientation. Some illustrative images are attached.
Any suggestions for how to correct this would be welcome.
Thank you, Cate
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