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