External Email - Use Caution Hi,
I am a bit noob on FreeSurfer and coordinate systems and I had a few questions. I am wondering if I have the T1.mgz file of FreeSurfer after running recon-all and this is the 256^3 image re-scaled and re-oriented from your orig.mgz file, then how does one define the fsnative (volume RAS) vs surface RAS (tkras in FreeSurfer)? Assuming there was no preprocessing done on the original scanner nifti, I run the following commands: (base) workstation$ mri_info ~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras -1.00000 0.00000 0.00000 126.81799 0.00000 -0.00000 1.00000 -121.57332 0.00000 -1.00000 0.00000 159.64563 0.00000 0.00000 0.00000 1.00000 (base) workstation$ mri_info ~/bids/derivatives/freesurfer/la02/mri/T1.mgz --vox2ras-tkr -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 *Questions:* 1. Applying the `vox2ras` to any voxel, I would get RAS xyz coordinates right? 2. If I apply `vox2ras-tkr` to any voxel, I would also get RAS xyz coordinates? 3. So what is the difference exactly between these two transforms? Is there anything special / consistent in terms of the definition of the origin and orientation? E.g. Orientation is always RAS, and origin is always... estimated center of the patient's brain? Or is the origin somewhere special like the AC? 3. When would I use one transform over the other? I've searched online and read through the following, but I feel like there is not explicit discussion of the above questions: - https://secure-web.cisco.com/1sKe3PERttYdO2z94AST1tBVsT1X0Q84dpaG1N3eU1eJEWBYAhaNffwjmetXvltBAVVoxL3wCTSrCoHakOkCugIkOyK117nI4W_o8Ym4a_y_4IMDdwzh7_GYB81jSdkXxD1sntK663LSCoBAmidk0lCKphKm-gu8jicKtMyP9nzEf6R6GUI7BAPifCPxG4Fd1Ag4GZj032qySdYH-cfZIQUhO2YozkmsTClbELucVqlx1WPRbuMUV1_LmmoMRtC_Qoe2LilELxRbTjuM1lx_1zA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems - http://secure-web.cisco.com/1fnkHZ6-zCUMYrDAnGdeklCU8ErX4aX7Dumo0EB8QRqeu1tchyVvKG13byw27nFcG79PvCIqOgGabwSblNBwYHTiUsLoHHqsI_3QPtWYk1gP3EOpMlMLI127WQ9EvNj6kI4PjGrBDj2k-ZSCy6AR_4p4jZx0Uajc3OlJpLRyX3VN6XhXzlOm8DVg3Matrv8aMkWJP414h9GEWcGyV35R9O7UlsD8r7bjcubNNXO-EjSk2QlxhXVwLT3HnvJaychce6XIlCfbNhzMzckkHjecW2w/http%3A%2F%2Fwww.grahamwideman.com%2Fgw%2Fbrain%2Ffs%2Fcoords%2Ffscoords.htm -- Best Regards, Adam Li (he/him) PhD Student in Biomedical Engineering Johns Hopkins University & School of Medicine
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