did you look at the help for mri_convert concerning the orientation?
On Sun, 16 Dec 2007, Ray Fix wrote:
Dear FS Listers,
mri_convert isn't giving me quite what I expected when I use it to reorient
an inhomogeneous volume. I apologize in advance if it is my misunderstanding
or something that has been covered before. These orientation issues make my
head spin (as they do the subject data ;-).
Consider the following example:
% mri_info volume.mgz
:
dimensions: 256 x 256 x 128
voxel sizes: 1., 1., 1.3300
:
Orientation : PIL
Primary Slice Direction: sagittal
:
I take this volume and reorient it with mri_convert to LIA orientation.
% mri_convert --out_orientation LIA volume.mgz volume_LIA.mgz
But what it gives me back is unexpected.
% mri_info volume_LIA.mgh
:
dimensions: 256 x 256 x 128
voxel sizes: 1., 1., 1.3300
:
Orientation : LIA
Primary Slice Direction: coronal
I was first surprised first that mri_convert was resorting to trilinear
interpolation. It seems like this kind of transformation could be done with
100% fidelity using nearest neighbor. But the bigger concern is I would have
also expected the output dimensions to be 128x256x256 with the voxel sizes
1.33, 1.00, 1.00. It seems like if you reorient a non cubic volume with
mri_convert, it arbitrarily cuts some of the data out from the posterior and
anterior. tkmedit display seems to confirm this.
To put it another way, I would expect:
mri_convert --out_orientation PIL volume_LIA.mgz volume_PIL.mgz
to generate at volume_PIL.mgz file that was voxel identical to the original
volume.mgz.
Thanks for your time.
Ray
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
