Hi Doug,
Thanks for clarifying this. My data is in Nifti-Format and looks fine in
FSLview, meaning that left is on the right-hand side of the screen and
vice versa. There is no qform orientation information in the header.
When I convert my data without --in_orientation LAS, it ends up looking
the wrong way round in tkmedit. When I convert as in
mri_convert --in_orientation LAS mydata.nii 001.mgz
it looks alright again, i.e. left is on the right-hand side of the
screen in tkmedit.
Now - having changed the orientation info, does that mean that I can
rely on the lh.* surfaces truly being the left hemisphere, as long as I
make sure that the 001.mgz input looks correct in tkmedit? Or is there
some more intricate problem with the orientation info that I am missing?
Thanks again,
Johannes
Doug Greve schrieb:
I think this has been fixed. BTW, be very careful changing the
orientation describtion. Note that it is the description that is being
chaanged, NOT the pixel data. If your pixel data were oriented one way
and the description was correct, changing the description will make the
description wrong.
doug
Johannes Klein wrote:
Hi folks,
There's a small bug in the online help for mri_convert I found when
trying to get my input Nifti's left/right to match with freesurfer
conventions.
When run without any parameters, the last paragraph describes the use
of the --in-orientation switch. That must read --in_orientation
(probably same for out-/out_).
Took me a while to figure that one out ;)
Cheers,
Johannes
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