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Hi experts,
A follow-up question: how to verify if the results (gtm.stats.dat) generated by
mri_gtmpvc make sense?
Thanks,
Angel
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of WONG Wan Wa
<angelw...@ust.hk>
Sent: Wednesday, April 10, 2024 5:16 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?
External Email - Use Caution
Thanks Michael!
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rullmann, Michael
<michael.rullm...@medizin.uni-leipzig.de>
Sent: Tuesday, April 9, 2024 7:27 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?
You can just google those values for each scanner.
For example:
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Second result links directly to the Siemens website:
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There, it is stated:
Transverse spatial resolution (NEMA 2012)
FWHM @ 1 cm : 4.6 mm
You can also determine the parameters yourself by following the NEMA standards.
Best
Michael
Von: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von WONG Wan Wa
Gesendet: Dienstag, 9. April 2024 12:03
An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Betreff: 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-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 WONG Wan Wa <angelw...@ust.hk<mailto:angelw...@ust.hk>>
Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET
data with single frame?
External Email - Use Caution
Any idea about the PSF?
________________________________
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 WONG Wan Wa <angelw...@ust.hk<mailto:angelw...@ust.hk>>
Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET
data with single frame?
External Email - Use Caution
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-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: Saturday, March 30, 2024 5:23 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: 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:
External Email - Use Caution
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-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: Thursday, March 21, 2024 9:44 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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:
External Email - Use Caution
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-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: Wednesday, March 20, 2024 11:27 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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:
External Email - Use Caution
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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