External Email - Use Caution Hi Yujing,
Apologies for the delayed response. I am running the command: recon-all -base <templateid> -tp <tp1id> -tp <tp2id> … -autorecon1 -notalcheck This works for all but two of my subjects where I get the issue I reported. How would I add the options you have suggested to my command line? Thank you, Nathan From: Huang, Yujing <yhuan...@mgh.harvard.edu> Date: Wednesday, 26 October 2022 at 18:38 To: Nathan Kindred (PGR) <n.kindr...@newcastle.ac.uk> Cc: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] Issue with rotation during longitudinal base creation ⚠ External sender. Take care when opening links or attachments. Do not provide your login details. Hi Nathan, Can you confirm that the error was from mri_robust_template? Not sure what your command line options. I think these options ‘—inittp <>’, ‘--fixtp’, ‘—seed <>’ might help. Best, Yujing -------- Forwarded Message -------- Subject: [Freesurfer] Issue with rotation during longitudinal base creation Date: Wed, 12 Oct 2022 16:54:29 +0000 From: Nathan Kindred (PGR) <n.kindr...@newcastle.ac.uk><mailto:n.kindr...@newcastle.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Hi, I have been processing longitudinal data using the longitudinal processing stream but for some subjects I am having getting this error when creating the base: Input rotation's max deviation from rotation is: 0.000258493 MyMatrix::RotationMean input(s) not rotation What would be the best way to fix this? Best, Nathan 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/1w2-5giZgGYsy5u-TRbt_J9p29bSuPPIuhjRFe-L1C-vorxcGbJkUV5YfWyvYKwO1Gi9b1A1rV1JoZ697Js26Jrqfb8aSpyTxe5xyEaJg-ChxQUd7dSbcD3Ey_rcVY0HOdjdGlHGLZ6sgEtQF-Gyz7Zff5_Raszas_MTlG2nRuyzYb8SfqgyfZ086tXJG8y7DhCkRnp5dxPtx1CVMPcZywB3Jg4YG72RrSJAKLuq88FFTM7Pf_-BygyKMU6qeRhNgmZh1RgYfqOYn13gupgN9qCjT7NpVA_IjQTyZHUwcu_dQZq2P0TG5X1YmYecpiGdJ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline<https://secure-web.cisco.com/14Rw9DkKkSSEDGScn9pf15Z31vcka5JQ67x775oMzp56iJSiJTuZJCltA59ymD1R-g1hxcTOAGHE5QznK8XG2UdgNKjxUywcIG5G0F4V6AsQPP3Bl9HX8jNrPVOC1lspR8bvGAKBOdzkN6ANi4KQ2XMAVaC2NrnbqHoJ4j1_56oZuH3SctobiyGjrntsy6vVmLm03sRm0diaP4sdLUJn79WIdRiwOQ8GgrjpdD2G6qX7CeOkytdyJdCnBavWPX1GEZSL6Wm8N5bNOsni0MqUjYOGi84b_vKNgt79jKtJs8TF2z91rvjPGbqYYxUBpRbLW/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D05%257C01%257CN.Kindred1%2540newcastle.ac.uk%257C575917b6ca254524097108dab778ebbf%257C9c5012c9b61644c2a91766814fbe3e87%257C1%257C0%257C638024027241262208%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DVnYyfNyzf5DwStHoQRTd9pUkoOFJAPdjopVF2SNHZC4%253D%26reserved%3D0> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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