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that is correct Doug - the 2nd recon-all batch had a better set of scans (intensity wise). For some reason the T1.mgz volumes are slightly translated from one another, as are the surfaces (in that image I attached) and it is creating the same issue with the labels when I use mri_label2label. Why would mri_label2label with registration method as surface be having this issue? How might I overcome this?

Thank you,

Trisanna

Trisanna Sprung-Much, PhD

Research Associate

McGill University

Montreal Neurological Institute

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, October 27, 2021 12:26 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_label2label issues

I'm not sure what you did or how to interpret that pic. If I understand, you ran a case through recon-all and created labels on that case. You then recon-all again using a totally different output where you improved the homogeneity. You now want to map the labels you created on the 1st run to the 2nd run. Is that right?

On 10/22/2021 4:58 PM, Trisanna Sprung-Much wrote:

External Email - Use Caution

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Hi there

I created labels on surfaces of subjects (chimp) registered to a particular volumetric template. The labels were created on the surfaces in Freeview using Freesurfer 7.1.

Since creating these labels, I improved the intensity inhomogeneity in the scans and re-ran the surfaces. When I try to use mri_label2label to transpose the labels to the new surfaces of each subject, the labels do not fall exactly where they should. In fact, the surfaces themselves have a slight translation in them (see snapshot). I assume this is because my registration to the template that I did prior to running recon-all is differing somehow between the 2 groups. However, I thought that this should not matter since mri_label2label --regmethod surface is using the sphere.reg to fsaverage.

I am wondering if there is anything I can do to improve mri_label2label to avoid editing the labels manually?

Thank you for your time,

Trisanna

--

Trisanna Sprung-Much, PhD

Research Associate

McGill University

Montreal Neurological Institute
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