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
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
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
Margaret,
orient_mri is a gui tool which can be used to re-orient a volume, visually. for help, see: https://surfer.nmr.mgh.harvard.edu/fswiki/orient_mri
Nick
On Wed, 2008-08-20 at 16:33 -0400, 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
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 mailto: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 <mailto: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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Margaret Sheridan -
Nick Schmansky