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 >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
