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.kindr...@newcastle.ac.uk>
Sent: Sunday, November 20, 2022 6:35 AM
To: Huang, Yujing <yhuan...@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Issue with rotation during longitudinal base creation
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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<mailto:yhuan...@mgh.harvard.edu>>
Date: Wednesday, 26 October 2022 at 18:38
To: Nathan Kindred (PGR)
<n.kindr...@newcastle.ac.uk<mailto:n.kindr...@newcastle.ac.uk>>
Cc: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: RE: [Freesurfer] Issue with rotation during longitudinal base creation
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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:
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<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>
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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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