Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Zhener Zhang]

External Email - Use Caution

Found it. Thank you very much!


Thanks,
ZZ


On Apr 26, 2022, 12:28 -0700, Zhener Zhang , wrote:
Thank you, Douglas!
Is it possible to extract the number of voxels in each segment [of the 
FreeSurfer DK atlas]?
We are hoping to ‘reverse’ the spatial averaging process to get the sum of 
expression level in each ROI.

Thanks,
ZZ
On Apr 25, 2022, 11:34 -0700, Zhener Zhang , wrote:
Hi Douglas,

Thanks! We ran the following for one of our subjects:
mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg 
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale --o 
~/sz013/gtmpvc.output

Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:
Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us to suspect 
that something was wrong. I was just curious as to the general process behind 
PETSurfer’s ROI-wise value calculation. Was each ROI-wise output generated by 
averaging across all voxels of an ROI?

Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:
Hello,

I have a question regarding the way ROI-wise values are calculated using 
PETSurfer.

We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small 
ROI like Putamen has one of the highest values of regional distribution of a 
PET tracer.

Is it the case that the PETSurfer ROI-wise value outputs were averaged, or 
normalized by each ROI’s volume? And what measure was divided, GM volume, 
number of voxels, or something else?

Thank you in advance!

Best regards,
Zhener

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Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

yes, in the gtm.stats file. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer for docs



On 4/26/2022 3:29 PM, Zhener Zhang wrote:


External Email - Use Caution

Thank you, Douglas!
Is it possible to extract the number of voxels in each segment [of the 
FreeSurfer DK atlas]?
We are hoping to ‘reverse’ the spatial averaging process to get the 
sum of expression level in each ROI.


Thanks,
ZZ
On Apr 25, 2022, 11:34 -0700, Zhener Zhang , wrote:

Hi Douglas,

Thanks! We ran the following for one of our subjects:

mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale
--o ~/sz013/gtmpvc.output


Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:

Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us 
to suspect that something was wrong. I was just curious as to the 
general process behind PETSurfer’s ROI-wise value calculation. Was 
each ROI-wise output generated by averaging across all voxels of an ROI?


Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a 
relatively small ROI like Putamen has one of the highest values of 
regional distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener



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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Zhener Zhang]

External Email - Use Caution

Thank you, Douglas!
Is it possible to extract the number of voxels in each segment [of the 
FreeSurfer DK atlas]?
We are hoping to ‘reverse’ the spatial averaging process to get the sum of 
expression level in each ROI.

Thanks,
ZZ
On Apr 25, 2022, 11:34 -0700, Zhener Zhang , wrote:
Hi Douglas,

Thanks! We ran the following for one of our subjects:
mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg 
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale --o 
~/sz013/gtmpvc.output

Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:
Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us to suspect 
that something was wrong. I was just curious as to the general process behind 
PETSurfer’s ROI-wise value calculation. Was each ROI-wise output generated by 
averaging across all voxels of an ROI?

Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:
Hello,

I have a question regarding the way ROI-wise values are calculated using 
PETSurfer.

We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small 
ROI like Putamen has one of the highest values of regional distribution of a 
PET tracer.

Is it the case that the PETSurfer ROI-wise value outputs were averaged, or 
normalized by each ROI’s volume? And what measure was divided, GM volume, 
number of voxels, or something else?

Thank you in advance!

Best regards,
Zhener

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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

In that case, it mapping the seg into the pet space (see aux/seg.nii.gz) 
and just averaging over the voxels in each segment.


On 4/25/2022 2:34 PM, Zhener Zhang wrote:


External Email - Use Caution

Hi Douglas,

Thanks! We ran the following for one of our subjects:

mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale
--o ~/sz013/gtmpvc.output


Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:

Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us 
to suspect that something was wrong. I was just curious as to the 
general process behind PETSurfer’s ROI-wise value calculation. Was 
each ROI-wise output generated by averaging across all voxels of an ROI?


Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a 
relatively small ROI like Putamen has one of the highest values of 
regional distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener



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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Zhener Zhang]

External Email - Use Caution

Hi Douglas,

Thanks! We ran the following for one of our subjects:
mri_gtmpvc --i sz013_BPnd.nii --reg sz013_BPnd.reg.lta --seg 
~/sz013/mri/gtmseg.mgz --default-seg-merge --no-tfe --no-rescale --o 
~/sz013/gtmpvc.output

Thanks,
ZZ
On Apr 24, 2022, 13:45 -0700, Zhener Zhang , wrote:
Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us to suspect 
that something was wrong. I was just curious as to the general process behind 
PETSurfer’s ROI-wise value calculation. Was each ROI-wise output generated by 
averaging across all voxels of an ROI?

Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:
Hello,

I have a question regarding the way ROI-wise values are calculated using 
PETSurfer.

We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small 
ROI like Putamen has one of the highest values of regional distribution of a 
PET tracer.

Is it the case that the PETSurfer ROI-wise value outputs were averaged, or 
normalized by each ROI’s volume? And what measure was divided, GM volume, 
number of voxels, or something else?

Thank you in advance!

Best regards,
Zhener

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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

There are several ways it might work depending upon how you ran it. This 
is why I was asking for your command line.


On 4/24/2022 4:46 PM, Zhener Zhang wrote:


External Email - Use Caution

Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us to 
suspect that something was wrong. I was just curious as to the general 
process behind PETSurfer’s ROI-wise value calculation. Was each 
ROI-wise output generated by averaging across all voxels of an ROI?


Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a 
relatively small ROI like Putamen has one of the highest values of 
regional distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener



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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Zhener Zhang]

External Email - Use Caution

Hi Douglas,

Thank you for the reply!

The mri_gtmpvc outputs were expected and there was no reason for us to suspect 
that something was wrong. I was just curious as to the general process behind 
PETSurfer’s ROI-wise value calculation. Was each ROI-wise output generated by 
averaging across all voxels of an ROI?

Thanks!
Zhener Zhang


On Apr 20, 2022, 09:50 -0700, Zhener Zhang , wrote:
Hello,

I have a question regarding the way ROI-wise values are calculated using 
PETSurfer.

We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small 
ROI like Putamen has one of the highest values of regional distribution of a 
PET tracer.

Is it the case that the PETSurfer ROI-wise value outputs were averaged, or 
normalized by each ROI’s volume? And what measure was divided, GM volume, 
number of voxels, or something else?

Thank you in advance!

Best regards,
Zhener

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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Douglas N. Greve]

Can you send your mri_gtmpvc command line?

On 4/20/2022 12:50 PM, Zhener Zhang wrote:


External Email - Use Caution

Hello,

I have a question regarding the way ROI-wise values are calculated 
using PETSurfer.


We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively 
small ROI like Putamen has one of the highest values of regional 
distribution of a PET tracer.


Is it the case that the PETSurfer ROI-wise value outputs were 
averaged, or normalized by each ROI’s volume? And what measure was 
divided, GM volume, number of voxels, or something else?


Thank you in advance!

Best regards,
Zhener


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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail. 

[Freesurfer] Does PETSurfer calculate ROI-wise values by averaging?

[Zhener Zhang]

External Email - Use Caution

Hello,

I have a question regarding the way ROI-wise values are calculated using 
PETSurfer.

We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively small 
ROI like Putamen has one of the highest values of regional distribution of a 
PET tracer.

Is it the case that the PETSurfer ROI-wise value outputs were averaged, or 
normalized by each ROI’s volume? And what measure was divided, GM volume, 
number of voxels, or something else?

Thank you in advance!

Best regards,
Zhener

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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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