External Email - Use Caution
Hi Bruce, Thank you so much for your reply! I got it.
Sincerely Haiyun
On Thu, Nov 10, 2022 at 5:08 PM Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> wrote:
Hi Haiyun
We reslice everything to coronal as part of the recon process. If you want to map it back to the original orientation I think something like this should work:
mri_convert -rt nearest -rl rawavg.mgz aseg.mgz aseg.original_orientation.mgz
cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Haiyun Chen *Sent:* Thursday, November 10, 2022 4:58 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] How to set original orientation for converted images
External Email - Use Caution *Hello FreeSurfer Experts,
I converted the aseg.mgz file to aseg.nii using mri_convert command,
the aseg.mgz file is located in the directory below based on your tutorial:
tutorial_data_20190918_1558/practice_with_data/Subj001/mri
When I open the file aseg.nii in a different application,
the original orientation is not sagittal.
In the MRI protocol, the original orientation is sagittal.
Could you please help to tell how to set the original orientation
of output images to be sagittal?
Thank you in advance!
Best regards
Haiyun
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1arkORvz3iOCEI-rbMWdth27BgnoePuJU-yCR1-tUIH_wlF... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1pMJOUDjzaTA4E6MPc79XgW01QJApkZdOHKuVFgQj5s0MzG... < https://secure-web.cisco.com/1pMJOUDjzaTA4E6MPc79XgW01QJApkZdOHKuVFgQj5s0MzG... .