External Email - Use Caution I tried `--conform-dc` and the flag was not recognized. `-conform-dc` didn't give me error. However, vox2ras-tkr still didn't include the cosine information.
This is the Torig: mri_info --vox2ras-tkr T1.mgz -1.00000 0.00000 0.00000 128.00000 0.00000 0.00000 1.00000 -128.00000 0.00000 -1.00000 0.00000 128.00000 0.00000 0.00000 0.00000 1.00000 While Norig is mri_info --vox2ras T1.mgz -0.99989 0.00604 0.01331 124.66034 0.01408 0.15990 0.98703 -164.17455 -0.00383 -0.98711 0.15997 108.14072 0.00000 0.00000 0.00000 1.00000 I wonder what steps I could take to make sure the Torig = Norig. Here Norig is acpc realigned. Best, - D On Mon, Jan 1, 2024 at 4:27 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > If you want to keep the original orientation, you can specify > --conform-dc. Would that fix your problem? > > On 12/21/2023 9:30 AM, Dipterix Wang wrote: > > External Email - Use Caution > Dear FreeSurer Wizards, > > I'm trying to run the recon-all command on one of my template brains such > that the resulting Norig and Torig are identical. I understand that fs > always conforms the MRI to 256^3 before segmentation. I wonder if there is > any way that I can resample the original MRI to achieve the same Norig and > Torig? > > More specifically, currently the Torig (vox to tkrRAS) is > [,1] [,2] [,3] [,4] > [1,] -1 0 0 128 > [2,] 0 0 1 -128 > [3,] 0 -1 0 128 > [4,] 0 0 0 1 > > If I resample the input image such that Norig (vox to scanRAS) equals this > matrix, can I expect that "conform" does not change the orientation? > > Alternatively, is there any method I can use to "predict" or reproduce the > Torig from the original MRI outside of FreeSurfer? > > Thanks, > - Dipterix > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1tO0Wjb5ekjKkkZoaygATt42ODvCqJv-XfhqZbSqJhF3k_DqJ3AvDnrzb4-gePxkeOniuXN1qCLi1te9y72vO-CjZ5kzsjwTCZJfbBLgc-5PMGpihhpoi43wiGjivVvqn8GJOHjLP4wbzoah1k5V5G4uNbSN_btPapte59dviDtT8fVsFjH28gnbxxxOefhcHBFeBk0Fhf5sFpVCD022L40M4sMJ3hgaPHrwC_35qqw3zyxu998ex3Vw1y96tPh3fwnBDt5wgPJlwf62n4ujAsHeQ4ju-knFjrJ2adI3ksk9xwp9Dyg4mIoRNnl8nlAVs1KfI4aEK6T0hDSPbfEOybA/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/1spdzsTy5nH-y6bhSLJq2Wcin8crxFnBzpkWIRA_IIjHmYPBOuvaB4rXPq6UzTLg3tOse1qRHOMX84rhL-lBre05-Xkw5Lez7NP3JRklv8eXC5we31aP4HYzd7kkVl-vF2sEaMadGrgn_BBHcfEo7oji4dWw6zVZ7w4eb-WwkJ0xrsTdaCCV4rfIofsnGPuDHzoyS2r1jT6Pnhz3k22iqS2vugOdvQa99vL39daDVCN4RDWkPfzgVKSWASt6yLelfhYeE6TFTH_ejdKAWais-OqC5GDU42jC6yofYOGw-pHRHP-Pp1n6cZi3OUKfvMu4vWZKJRaEQR9fouJHCCtzRhw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1spdzsTy5nH-y6bhSLJq2Wcin8crxFnBzpkWIRA_IIjHmYPBOuvaB4rXPq6UzTLg3tOse1qRHOMX84rhL-lBre05-Xkw5Lez7NP3JRklv8eXC5we31aP4HYzd7kkVl-vF2sEaMadGrgn_BBHcfEo7oji4dWw6zVZ7w4eb-WwkJ0xrsTdaCCV4rfIofsnGPuDHzoyS2r1jT6Pnhz3k22iqS2vugOdvQa99vL39daDVCN4RDWkPfzgVKSWASt6yLelfhYeE6TFTH_ejdKAWais-OqC5GDU42jC6yofYOGw-pHRHP-Pp1n6cZi3OUKfvMu4vWZKJRaEQR9fouJHCCtzRhw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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