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Hi there

Just wanted to follow up on this as I am still dealing with this issue and would love to avoid having to edit all labels.

Thank you! Trisanna

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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 Trisanna Sprung-Much trisanna.sprung-much@mail.mcgill.ca Sent: Wednesday, October 27, 2021 12:39 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2label issues

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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

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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

External Email - Use Caution

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1q5tLeMBonQ68z0n88Yl920FIxC8aFXA_OZHvYSqEM50UX8...

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Hi Doug

I did and I responded with the following:

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 to avoid redrawing my labels?

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, November 3, 2021 11:08 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2label issues

Did you see this response from a few days ago?

On 10/27/2021 11:26 AM, Douglas N. Greve wrote: 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

External Email - Use Caution

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1q5tLeMBonQ68z0n88Yl920FIxC8aFXA_OZHvYSqEM50UX8...

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Hi Doug

THIS WORKED!!! Thank you so much for all your help!

Trisanna

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________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, November 8, 2021 1:35 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2label issues

Try this: register the old/1st recon to the second with bbregister --mov old/mri/nu.mgz --targ newsubject --t1 --reg reg.lta Map the old surface into the new space mris_apply_reg --lta reg.lta old/surf/lh.white newsubject/surf/lh.white.old Verify that the old surface overlays on the new volume Map the old labels onto the new volume with mris_apply_reg --src-label old/label/lh.your.label --streg newsubject/surf/lh.white.old newsubject/surf/lh.white --o newsubject/label/lh.your.label

On 11/3/2021 10:17 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

External Email - Use Caution

Hi Doug

I did and I responded with the following:

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 to avoid redrawing my labels?

Thank you,

Trisanna

--

Trisanna Sprung-Much, PhD Research Associate McGill University Montreal Neurological Institute ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Wednesday, November 3, 2021 11:08 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2label issues

Did you see this response from a few days ago?

On 10/27/2021 11:26 AM, Douglas N. Greve wrote: 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

External Email - Use Caution

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1q5tLeMBonQ68z0n88Yl920FIxC8aFXA_OZHvYSqEM50UX8...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1XDipzTNqR-eyZ5-ak_UQjLWy90oTiBf1ZBMWlxLvtvriJ-...