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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 zhener@stanford.edu, 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 zhener@stanford.edu, 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

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 zhener@stanford.edu, 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 zhener@stanford.edu, 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 zhener@stanford.edu, 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

External Email - Use Caution

Found it. Thank you very much!

Thanks, ZZ

On Apr 26, 2022, 12:28 -0700, Zhener Zhang zhener@stanford.edu, 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 zhener@stanford.edu, 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 zhener@stanford.edu, 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 zhener@stanford.edu, 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