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 < [email protected]> 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:* [email protected] < > [email protected]> *On Behalf Of *Haiyun Chen > *Sent:* Thursday, November 10, 2022 4:58 PM > *To:* Freesurfer support list <[email protected]> > *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 > [email protected] > https://secure-web.cisco.com/1arkORvz3iOCEI-rbMWdth27BgnoePuJU-yCR1-tUIH_wlFyvOQez-ampNFynb-bgTuQ24exxLv8ilqDHjMdfFbo9pdzpwRUPbLo-d3frOghmG0MstqzBnzKH2zFtdud54WQb4d8CNOjG7h-GAANo1Qudihf_aNZpy5VSreeZ8yyuY0Rq3plbeOPse0i8LL-s6492lk8dq8SIsxC7CqywLtxuYV7H7CEtdOQf4thS7-dDb4NHWKoN6CUUoPAjdVJ2RZasofNmKKy2iKq285qbaraAVcSwR7L8S6PTcZUaVKR7H8_QD4cXGrJ-XFb1fkJ2AwRzBUGOtJbSjCUr6BQYBw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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/1pMJOUDjzaTA4E6MPc79XgW01QJApkZdOHKuVFgQj5s0MzGY6BdZ-eOwqfXZlp2J0MmGqlKMfPY4oYvg56yNf9JJo8esGjk4xiSwdo_4x2qszpN0HygVLPNgPtlzDVjW6MyKOG4aPBM5Gdb2JVuoIHk-wrwzWK4fO7K2J1U0YjC_J-hBNHU0s5U1Jk0rObBSFBqFo91m80gHxaM8nsHOog9pKQxo6Y0ddc25omokfmBMIzuD_hYwxhr5299_G0mPLIfjj6G1NIGH27ASlnVuKk_2JB4EkqpSCrTAY7ozBKrn54_tR25CmxKs1v6j8i8T_4OMQKPDg18pg29Vb0hts4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1pMJOUDjzaTA4E6MPc79XgW01QJApkZdOHKuVFgQj5s0MzGY6BdZ-eOwqfXZlp2J0MmGqlKMfPY4oYvg56yNf9JJo8esGjk4xiSwdo_4x2qszpN0HygVLPNgPtlzDVjW6MyKOG4aPBM5Gdb2JVuoIHk-wrwzWK4fO7K2J1U0YjC_J-hBNHU0s5U1Jk0rObBSFBqFo91m80gHxaM8nsHOog9pKQxo6Y0ddc25omokfmBMIzuD_hYwxhr5299_G0mPLIfjj6G1NIGH27ASlnVuKk_2JB4EkqpSCrTAY7ozBKrn54_tR25CmxKs1v6j8i8T_4OMQKPDg18pg29Vb0hts4A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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