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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Thursday, March 21, 2024 9:44 PM
*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?
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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