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: 1.0000, 1.0000, 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: 1.0000, 1.0000, 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