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

 

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

Reply-To:

Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

To:

freesurfer@nmr.mgh.harvard.edu <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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