You can try using mri_convert with the -iid, -ijd, and -ikd options. I'll warn you now, this is not a fun thing to do, but once you figure it out for one, you can probably script it with the rest. The middle letter indicates the direction that is being manipulated. "i" is for left right, "j" is for sup-inf, and "k" is for ant-post. So, you can run something like:


mri_convert your.img new.mgz -iid -1 0 0 -ijd 0 -1 0 -ikd 0 0 1

To experiment with it, you'll need to follow some rules:
1. You can change the signs of the 1s
2. Each triple should have two 0s and one +/-1
3. No triple should be the same as another triple

You can play around with it by swapping triples and changing signs. Good luck!

doug


Margaret Sheridan wrote:
Bruce,
 
Yeah, I know about that danger. We are doing this on brains where we have a marker - a vitamin e capsule on the left side of the forehead. I'm most concerned about learning how to rotate the brains at all, right at the moment.
 
Thanks (for the concern as well),
 
Margaret
 
On 8/20/08, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Margaret and Kathy,

you *really* don't want to be trying to guess the orientation yourself as you are likely to get left/right wrong. Avi: have you moved data back and forth into freesurfer?
cheers
Bruce




On Wed, 20 Aug 2008, Margaret Sheridan wrote:

We are new users of freesurfer (linux v 4.0.5) and have the following
question:

We have some .4dfp.img MPRAGE files which we are trying to use (from Wash
U). When we run recon_all (1st step) or mri_convert on its own, the brain
comes up upside down as if it was rotated 180 degrees around the sagital
plane (see attached picture of the 4dfp.img file viewed in scuba). Since
when we view the original 4dfp.img file or the orig.mgz file they are both
in this orientation it appears that this is a problem with the original
files.

If we use tkmedit to rotate the brain around the sagital plane once we're in
.mgz format the recon steps (including normalization which, obviously, would
fail previously when the brain was upside down) would complete fine. However
I'd prefer to rotate these brains using mri_convert (or another program) so
I can rotate the original files; which is why I'm writing now.

To determine what the current orientation for these images was I opened the
original files in scuba & ran MRI convert like this:
mri_convert --in_orientation ASL -i vcXXX.4dfp.img --out_orientation ASL -o
vcXXX.4dfp.ASL.img

until I found an orientation which matched the original. The orientation
which matched the original was ASL. In this step I just converted from one
form to the same form to reduce confusion.

Next I ran several versions of the following:
mri_convert --in_orientation ASL -i vcXXX.4dfp.img --out_orientation SAR -o
vcXXX.4dfp.SAR.img

however no mater how I changed the 'out orientation' when the files were
viewed in scuba they all appeared to have the same orientation as the
original (ASL or rotated around the sagital plane).

Is there any more documentation on re-orienting in mri_convert or does
anyone have any ideas/experience that can help?

Thanks,
Margaret Sheridan
Kathy Zhang

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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