Hi Nathan,

I don’t see recon-all taking any options for mri_robust_template.

You can try to run mri_robust_template on those two subjects outside recon-all.

Can you send us some data to debug if it is possible?

Thanks.

Yujing

From: Nathan Kindred (PGR) N.Kindred1@newcastle.ac.uk Sent: Sunday, November 20, 2022 6:35 AM To: Huang, Yujing YHUANG43@mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Issue with rotation during longitudinal base creation

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 <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Wednesday, 26 October 2022 at 18:38 To: Nathan Kindred (PGR) <N.Kindred1@newcastle.ac.ukmailto:N.Kindred1@newcastle.ac.uk> Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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.Kindred1@newcastle.ac.ukmailto:N.Kindred1@newcastle.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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

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