Hi Victor,

I'm trying to understand what you described, and re-produce it here. Which .annot are you referring to? Also, can you provide the command sequences that you used to generate mpm.vpnl+aseg.mgz?

Thanks.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Zeng, Victor (BIDMC - Keshavan - Psychiatry) Sent: Tuesday, November 8, 2022 4:05 PM To: freesurfer@nmr.mgh.harvard.edu Cc: jsritharan@student.ethz.ch Subject: Re: [Freesurfer] [External] Re: Mapping the labels onto the aparc atlas

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Hi,

I'm assuming the .annot is wrong because it doesn't map the entire gray matter ribbon, whereas when the .annot is mapped unto the gray matter ribbon using mri_aparc2aseg, its grabbing the surround gray matter. I am attaching a picture as illustration. This is the rh FG4 (from the Stanford atlas), in the sagittal view. The yellow is the .label file for the FG4, and when its mapped unto the gray matter, the brown region is mapped as the FG4. Is this the procedure that's suppose to happen?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ 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: Tuesday, November 8, 2022 9:14 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Mapping the labels onto the aparc atlas

I'm not sure what you are saying. Are you saying that the annot/surf looks right but the seg in the volume looks wrong or that they both look wrong? On 10/31/2022 2:58 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

External Email - Use Caution Hi Freesurfer devs,

We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the corresponding voxels that the labels identify as the mpm/vpnl. Can we reliably use the mpm.vpnl+aseg.mgz, and are the stats created from that file, or from the annot file? We are asking because we are using the mpm.vpnl+aseg.mgz as a mask for blood perfusion measurements.

Thanks,

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Hi all, I just want to follow up with this email since it has been a while with no replies. Thanks

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: Zeng, Victor (BIDMC - Keshavan - Psychiatry) vzeng@bidmc.harvard.edu Sent: Wednesday, November 9, 2022 1:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: jsritharan@student.ethz.ch jsritharan@student.ethz.ch Subject: Re: [External] Re: [Freesurfer] [External] Re: Mapping the labels onto the aparc atlas

We are using the command:

mri_aparc2aseg --s bert --annot mpm.vpnl

on FS7.1.0 in linux. This creates the mpm.vpnl+aseg.mgz in the mri folder.

We are referring to the mpm.vpnl.annot.

A little bit more context is that we have ASL images, that we are trying to generate a mpm+vpnl map for. We are trying to convert from .annot to .mgz so that we can grab the mean regional CBF for each mpm+vpnl region

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Wednesday, November 9, 2022 8:18 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: jsritharan@student.ethz.ch jsritharan@student.ethz.ch Subject: [External] Re: [Freesurfer] [External] Re: Mapping the labels onto the aparc atlas

Hi Victor,

I’m trying to understand what you described, and re-produce it here. Which .annot are you referring to? Also, can you provide the command sequences that you used to generate mpm.vpnl+aseg.mgz?

Thanks.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Zeng, Victor (BIDMC - Keshavan - Psychiatry) Sent: Tuesday, November 8, 2022 4:05 PM To: freesurfer@nmr.mgh.harvard.edu Cc: jsritharan@student.ethz.ch Subject: Re: [Freesurfer] [External] Re: Mapping the labels onto the aparc atlas

External Email - Use Caution

Hi,

I'm assuming the .annot is wrong because it doesn't map the entire gray matter ribbon, whereas when the .annot is mapped unto the gray matter ribbon using mri_aparc2aseg, its grabbing the surround gray matter. I am attaching a picture as illustration. This is the rh FG4 (from the Stanford atlas), in the sagittal view. The yellow is the .label file for the FG4, and when its mapped unto the gray matter, the brown region is mapped as the FG4. Is this the procedure that's suppose to happen?

Victor Zeng

Beth Israel Deaconess Medical Center

Keshavan Lab

--

________________________________

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: Tuesday, November 8, 2022 9:14 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Mapping the labels onto the aparc atlas

I'm not sure what you are saying. Are you saying that the annot/surf looks right but the seg in the volume looks wrong or that they both look wrong?

On 10/31/2022 2:58 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

External Email - Use Caution

Hi Freesurfer devs,

We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the corresponding voxels that the labels identify as the mpm/vpnl. Can we reliably use the mpm.vpnl+aseg.mgz, and are the stats created from that file, or from the annot file? We are asking because we are using the mpm.vpnl+aseg.mgz as a mask for blood perfusion measurements.

Thanks,

Victor Zeng

Beth Israel Deaconess Medical Center

Keshavan Lab

--

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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

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