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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
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Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
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