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
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