I've recently changed the way we handle nifti to read and write both the
qform and sform, so it should be (more) comptatible with fsl. If it
"looks right" in tkmedit, then you have the geometry correct, and
freesurfer will respect that. But you have to make sure that you know
which side is left/right in your image, which is very difficult to do if
you did not use a fiducial. The subject's left side should show up on
the right side of the image in tkmedit. You may want to use mri_convert
to convert from your dicom into nifti or mgz for further processing in
freesurfer.
doug
Johannes Klein wrote:
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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