Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

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How to determine the PSF? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WONG Wan Wa angelwong@ust.hk Sent: Friday, April 5, 2024 12:14 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

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Any idea about the PSF? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WONG Wan Wa angelwong@ust.hk Sent: Tuesday, April 2, 2024 12:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

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Hi Douglas,

Here is the information given by the technician from the PET center:

There are a total of 3 machines used for PIB PET/CT or PET/MR scans

1. PET/CT1 ( mCT)(contain "mCT" in the pet series)

Manufacturer: Siemens ManufacturersModelName: Biograph128_mCT recon method : TrueX + TOF (ultra HD-PET) iteration: 5 subset:21 matrix: 400x400 zoom: 2.0 Gaussian filter FWHM: 2.0mm

1. PET/CT2 (Vision)(contain "Vis" in the pet series) Manufacturer: Siemens ManufacturersModelName: Biograph128Edge_Vision 600

recon method: TrueX + TOF (ultra HD-PET) iteration: 8 subset: 5 matrix: 512x512 zoom: 2.0 Gaussian filter FWHM: 2.0mm

1. PET/MR (mMR)

Manufacturer: Siemens ManufacturersModelName: Biograph_mMR recon method: HD-PET iteration: 5 subset: 21 matrix: 344x344 zoom:2.0 Gaussian filter FWHM:2.0mm

Thanks, Angel

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Sent: Saturday, March 30, 2024 5:23 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

That 2mm for the gaussian is just the post-processing filter and does not represent the full amount of partial volume effect. What kind of scanner is it?

On 3/22/2024 12:42 AM, WONG Wan Wa wrote:

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Hi Douglas,

Thanks for your clarification. This is my first time to run PetSurfer. We did want to normalize by cerebellar grey matter, and I will add the "--rescale 8 47". I just copied "6" from the example command. I know "6" should be the FWHM of the point-spread function (PSF) of the scanner as measured in image space. I did ask the technician at the PET centre, and he replied that the reconstruction method was "OP-OSEM 8i21s" and the filter was "XYZ gaussian 2.00". Can I use "2" for psf in the command?

Thanks, Angel

________________________________ 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: Thursday, March 21, 2024 9:44 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

Yes, though that will normalize by the pons. If you want to normalize by something else, you will need to specify it with --rescale. Eg, if you want to normalize by ceberbellar gray matter, add --rescale 8 47 Where did you get "6" from for the psf?

On 3/20/2024 10:57 PM, WONG Wan Wa wrote:

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Hi Douglas,

Thanks for your reply. We used different tracers for diagnosis of AD or other neurodegenerative diseases, including PIB, FDG, Flutemetamol and TAU. If an SUV analysis is used, is it done by mri_gtmpvc? Is there any subsequent analysis needed?

This is my mri_gtmpvc command: mri_gtmpvc \ --i $SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.nii.gz \ --reg $SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.reg.lta \ --psf 6 \ --seg $SUBJECTS_DIR/sub-QM001/mri/gtmseg.mgz \ --default-seg-merge \ --auto-mask 1 .01 \ --mgx .01 \ --o $SUBJECTS_DIR/sub-QM001/pet/gtmpvc.output

Is this command okay?

Thanks, Angel

________________________________ 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: Wednesday, March 20, 2024 11:27 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

you cannot apply kinetic modeling to one frame. What is you ligand? For a one frame acquisition, you usually use an SUV analysis.

On 3/20/2024 12:03 AM, WONG Wan Wa wrote:

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Hi experts,

As stated in the subject, can kinetic modeling be applied to PET data with only one frame? Or we just stop at ROI analysis without kinetic modeling?

Best, Angel

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