Hi,
Just resending as I sent this at the end of the day Friday. Also, if this is difficult to correct, for whatever reason, then could you just let me know whether these mislabeled orientations will cause problems later in the processing stream.
Resent reply below:
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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