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Dear team,
We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC).
Thank you, Sneha
External Email - Use Caution
Dear team,
I wanted to follow up on the following question. Thank you.
Regards, Sneha
From: Sneha Pandya Sent: Tuesday, August 27, 2024 12:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: petsurfer using brainstem subfields
Dear team,
We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC).
Thank you, Sneha
It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg.ctab after running gtmseg). You can then specify the new seg with --seg to mri_gtmpvc. How well it works is another question. The smaller the ROI, the harder it is to do the PVC. It will give you an answer, probably without complaining, but it might not be an accurate one.
On 9/18/2024 10:40 PM, Sneha Pandya wrote:
External Email - Use Caution
Dear team,
I wanted to follow up on the following question. Thank you.
Regards,
Sneha
*From:*Sneha Pandya *Sent:* Tuesday, August 27, 2024 12:22 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* petsurfer using brainstem subfields
Dear team,
We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC).
Thank you,
Sneha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you Doug,
Just to clarify, do we superimpose on aparc+aseg or gtmseg? I believe subfileds and gtmseg would have same resolution.
If not combining subfields can we superimpose just one segmentation (in particularly we are interested in inferior colliculi, which freesurfer segments -> 7100 , Brainstem-inferior-colliculus as in FreeSurferColorLUT.txt) to gtmseg with suggested approach? If so can we just resample this segmentation to gtmseg resolution and the combine it?
On a separate note, when we run mri_gtmpvc with save-input flag, input.nii.gz is not pvc’ed at all right, like not even gtm which is default even when other PVC and tfe is turned off?
Regards, Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, September 20, 2024 9:36 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem subfields
It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg. ctab after running gtmseg).
It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg.ctab after running gtmseg). You can then specify the new seg with --seg to mri_gtmpvc. How well it works is another question. The smaller the ROI, the harder it is to do the PVC. It will give you an answer, probably without complaining, but it might not be an accurate one. On 9/18/2024 10:40 PM, Sneha Pandya wrote:
External Email - Use Caution Dear team,
I wanted to follow up on the following question. Thank you.
Regards, Sneha
From: Sneha Pandya Sent: Tuesday, August 27, 2024 12:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: petsurfer using brainstem subfields
Dear team,
We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC).
Thank you, Sneha
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On 9/20/2024 9:54 AM, Sneha Pandya wrote:
External Email - Use Caution
Thank you Doug,
Just to clarify, do we superimpose on aparc+aseg or gtmseg? I believe subfileds and gtmseg would have same resolution.
I don't think they are the same reg as gtmseg should be 0.5mm, but you can run mri_vol2vol --regheader --mov subfields.mgz --targ gtmseg.mgz --interp nearest --o subfields-in-gtmseg.mgz
If not combining subfields can we superimpose just one segmentation (in particularly we are interested in inferior colliculi, which freesurfer segments -> 7100 , Brainstem-inferior-colliculus as in FreeSurferColorLUT.txt) to gtmseg with suggested approach? If so can we just resample this segmentation to gtmseg resolution and the combine it?
Yes, that is the gist. You will probably want to make sure that there is no hippocampus voxels in the output; there could be because of edge effects. I don't think we seg colliculus unless it is one of the newer segs (just because it is in the LUT does not mean we segment it).
On a separate note, when we run mri_gtmpvc with save-input flag, input.nii.gz is not pvc’ed at all right, like not even gtm which is default even when other PVC and tfe is turned off?
Correct. I think it may just be rescaled. You can use mueller-gartner (--mgx) to voxel-wise pvc of GM
Regards,
Sneha
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Friday, September 20, 2024 9:36 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem subfields
It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg. ctab after running gtmseg).
It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg.ctab after running gtmseg). You can then specify the new seg with --seg to mri_gtmpvc. How well it works is another question. The smaller the ROI, the harder it is to do the PVC. It will give you an answer, probably without complaining, but it might not be an accurate one.
On 9/18/2024 10:40 PM, Sneha Pandya wrote:
* External Email - Use Caution * Dear team, I wanted to follow up on the following question. Thank you. Regards, Sneha *From:*Sneha Pandya *Sent:* Tuesday, August 27, 2024 12:22 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* petsurfer using brainstem subfields Dear team, We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC). Thank you, Sneha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://urldefense.com/v3/__https:/mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer__;!!Aer6R9v1Nk4!75aEon3A11KK_7tx-62JmBHCWyEvMftSDpswCNgAksXldC_JVea1U3ITU5t4Ba9JgjSy3QySBFtYbjnPqL2F7YbKiBmsvg$>
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Thank you Doug.
Regards, Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Monday, September 30, 2024 10:42 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem subfields
On 9/20/2024 9: 54 AM, Sneha Pandya wrote: External Email - Use Caution Thank you Doug, Just to clarify, do we superimpose on aparc+aseg or gtmseg? I believe subfileds and gtmseg would have same resolution. I don't think they are the same reg
On 9/20/2024 9:54 AM, Sneha Pandya wrote:
External Email - Use Caution Thank you Doug,
Just to clarify, do we superimpose on aparc+aseg or gtmseg? I believe subfileds and gtmseg would have same resolution. I don't think they are the same reg as gtmseg should be 0.5mm, but you can run mri_vol2vol --regheader --mov subfields.mgz --targ gtmseg.mgz --interp nearest --o subfields-in-gtmseg.mgz
If not combining subfields can we superimpose just one segmentation (in particularly we are interested in inferior colliculi, which freesurfer segments -> 7100 , Brainstem-inferior-colliculus as in FreeSurferColorLUT.txt) to gtmseg with suggested approach? If so can we just resample this segmentation to gtmseg resolution and the combine it? Yes, that is the gist. You will probably want to make sure that there is no hippocampus voxels in the output; there could be because of edge effects. I don't think we seg colliculus unless it is one of the newer segs (just because it is in the LUT does not mean we segment it).
On a separate note, when we run mri_gtmpvc with save-input flag, input.nii.gz is not pvc’ed at all right, like not even gtm which is default even when other PVC and tfe is turned off? Correct. I think it may just be rescaled. You can use mueller-gartner (--mgx) to voxel-wise pvc of GM
Regards, Sneha
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 Sent: Friday, September 20, 2024 9:36 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] petsurfer using brainstem subfields
It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg. ctab after running gtmseg). It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg.ctab after running gtmseg). You can then specify the new seg with --seg to mri_gtmpvc. How well it works is another question. The smaller the ROI, the harder it is to do the PVC. It will give you an answer, probably without complaining, but it might not be an accurate one. On 9/18/2024 10:40 PM, Sneha Pandya wrote:
External Email - Use Caution Dear team,
I wanted to follow up on the following question. Thank you.
Regards, Sneha
From: Sneha Pandya Sent: Tuesday, August 27, 2024 12:22 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: petsurfer using brainstem subfields
Dear team,
We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC).
Thank you, Sneha
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Sneha Pandya