Was the log file helpful? Sorry to be so persistent with this, but
I'm leaving tomorrow for two weeks and was hoping to be able to run
autorecon2 and 3 while I'm away, but as this is already causing
problems in autorecon1 (bad talaraich reg), I don't think I should go
any further until I correct this.
Just to reiterate, the 00? files are fine, but the rawavg.mgz has the
coronal and sagittal orientations swapped and in horizontal, the
anterior pole points left.
Thanks,
Cate
On Jun 18, 2007, at 11:45 AM, Bruce Fischl wrote:
Hi Cate,
so the 00?.mgz volumes show up fine in tkmedit, but the rawavg.mgz
doesn't? Can you send us the recon-all.log file?
Bruce
On Mon, 18 Jun 2007, Catherine Hartley wrote:
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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