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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
Sent: Wednesday, November 9, 2022 8:18 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: jsritha...@student.ethz.ch <jsritha...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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: jsritha...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
Sent: Tuesday, November 8, 2022 9:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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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