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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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Wednesday, March 20, 2024 11:27 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?
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-9ZHbGqylmDU85cPUM8os3pdf--t9YtoQYPlSEnzu1nuvW...
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.outputIs this command okay?
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:* Wednesday, March 20, 2024 11:27 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? 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1-9ZHbGqylmDU85cPUM8os3pdf--t9YtoQYPlSEnzu1nuvW1HsRPiVQBorKHh1b4-3Mq9oTlVrf34TXHCs8oJWmw1Zxj0E2diVIvuVYIGmHbzw2Q1XTmsoGxh2kynCpZjrwjhbeFW2Zx6B0x0dchfWvYZ18DZuslZpMu1jeD_b7LmIZ7S51sx7q8oU1015etWkwiumkMeXSLLLiGRef88_dPBVgR2YI6HRgPdt7bb7081CQqhUFgkf_yeE1yrsv4bGKrXDKPFZvusQ-DL6jyKLFSzJ46_BIcPgDXiC1zRQecChefLoaxkI15kNBHTFHIc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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-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:
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/18H3nt2GY4Mc_yll5PG4ZCrPhqsO8YRx8tItmeIgG90iAyf...https://secure-web.cisco.com/1-9ZHbGqylmDU85cPUM8os3pdf--t9YtoQYPlSEnzu1nuvW1HsRPiVQBorKHh1b4-3Mq9oTlVrf34TXHCs8oJWmw1Zxj0E2diVIvuVYIGmHbzw2Q1XTmsoGxh2kynCpZjrwjhbeFW2Zx6B0x0dchfWvYZ18DZuslZpMu1jeD_b7LmIZ7S51sx7q8oU1015etWkwiumkMeXSLLLiGRef88_dPBVgR2YI6HRgPdt7bb7081CQqhUFgkf_yeE1yrsv4bGKrXDKPFZvusQ-DL6jyKLFSzJ46_BIcPgDXiC1zRQecChefLoaxkI15kNBHTFHIc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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.outputIs this command okay?
Thanks, Angel
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1-9ZHbGqylmDU85cPUM8os3pdf--t9YtoQYPlSEnzu1nuvW1HsRPiVQBorKHh1b4-3Mq9oTlVrf34TXHCs8oJWmw1Zxj0E2diVIvuVYIGmHbzw2Q1XTmsoGxh2kynCpZjrwjhbeFW2Zx6B0x0dchfWvYZ18DZuslZpMu1jeD_b7LmIZ7S51sx7q8oU1015etWkwiumkMeXSLLLiGRef88_dPBVgR2YI6HRgPdt7bb7081CQqhUFgkf_yeE1yrsv4bGKrXDKPFZvusQ-DL6jyKLFSzJ46_BIcPgDXiC1zRQecChefLoaxkI15kNBHTFHIc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
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-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:
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-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:
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1CWR3NNy5GVUV5IIglmOQCCqPix2O5hMr0sFjMDjNX4Rtkq...https://secure-web.cisco.com/1-9ZHbGqylmDU85cPUM8os3pdf--t9YtoQYPlSEnzu1nuvW1HsRPiVQBorKHh1b4-3Mq9oTlVrf34TXHCs8oJWmw1Zxj0E2diVIvuVYIGmHbzw2Q1XTmsoGxh2kynCpZjrwjhbeFW2Zx6B0x0dchfWvYZ18DZuslZpMu1jeD_b7LmIZ7S51sx7q8oU1015etWkwiumkMeXSLLLiGRef88_dPBVgR2YI6HRgPdt7bb7081CQqhUFgkf_yeE1yrsv4bGKrXDKPFZvusQ-DL6jyKLFSzJ46_BIcPgDXiC1zRQecChefLoaxkI15kNBHTFHIc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
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?
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-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:
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-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:
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-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:
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZYjHWkiktL9IPHRZJA5aNUH4p62JD06k2fn15scWnDo5hf...https://secure-web.cisco.com/1-9ZHbGqylmDU85cPUM8os3pdf--t9YtoQYPlSEnzu1nuvW1HsRPiVQBorKHh1b4-3Mq9oTlVrf34TXHCs8oJWmw1Zxj0E2diVIvuVYIGmHbzw2Q1XTmsoGxh2kynCpZjrwjhbeFW2Zx6B0x0dchfWvYZ18DZuslZpMu1jeD_b7LmIZ7S51sx7q8oU1015etWkwiumkMeXSLLLiGRef88_dPBVgR2YI6HRgPdt7bb7081CQqhUFgkf_yeE1yrsv4bGKrXDKPFZvusQ-DL6jyKLFSzJ46_BIcPgDXiC1zRQecChefLoaxkI15kNBHTFHIc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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External Email - Use Caution
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?
External Email - Use Caution
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?
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-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:
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-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:
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-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:
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/17Of_5jEL6RLKd_i2syyml5DJbXC0x2MPX6f5h7JGtzmeZe...https://secure-web.cisco.com/1-9ZHbGqylmDU85cPUM8os3pdf--t9YtoQYPlSEnzu1nuvW1HsRPiVQBorKHh1b4-3Mq9oTlVrf34TXHCs8oJWmw1Zxj0E2diVIvuVYIGmHbzw2Q1XTmsoGxh2kynCpZjrwjhbeFW2Zx6B0x0dchfWvYZ18DZuslZpMu1jeD_b7LmIZ7S51sx7q8oU1015etWkwiumkMeXSLLLiGRef88_dPBVgR2YI6HRgPdt7bb7081CQqhUFgkf_yeE1yrsv4bGKrXDKPFZvusQ-DL6jyKLFSzJ46_BIcPgDXiC1zRQecChefLoaxkI15kNBHTFHIc/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/17Of_5jEL6RLKd_i2syyml5DJbXC0x2MPX6f5h7JGtzmeZe...https://secure-web.cisco.com/1CWR3NNy5GVUV5IIglmOQCCqPix2O5hMr0sFjMDjNX4RtkquqLXblWpg5PtckTC_1nsvptcuX1tbGy67KwKaz9cE2cM8v9hEraiCAE2Eh7KItQcXWE0-7Gmm_5io482z3Et5hrRly4j_KDzde5apC9qwTNAEUMEcFThYaTy3_GVG5D45FlNb6cpLYZDNjcRT_bH185Yv-DUDNzN5wxeySnlD7Bj6-4WAc8sOpl-TnUdLUdijJVsHoaNHqQa-zQTxclQhmq7zgEUDEbEZTBsmHI1Xa8g9OdMyrXSVShTrmLjVr9vjlW_sqcj_wL-PMsUKSS__xNhMyaKgJmT0UIGQ1sw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
You can just google those values for each scanner.
For example:
https://secure-web.cisco.com/1XqX9-a2LU-Yqo_eubkdqqmahVQPBMg1MvLiOSxV5SHgUNo...
Second result links directly to the Siemens website:
https://secure-web.cisco.com/1nbS9Vytnf798M-69hNgHUf9LyYJC4rkYI4w5c0QOt-Xd4n...
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of WONG Wan Wa <angelwong@ust.hk mailto:angelwong@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of WONG Wan Wa <angelwong@ust.hk mailto:angelwong@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
2. 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
4. 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 mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU mailto:dgreve@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve mailto:dgreve@MGH.HARVARD.EDU dgreve@MGH.HARVARD.EDU Sent: Thursday, March 21, 2024 9:44 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto: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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve mailto:dgreve@mgh.harvard.edu dgreve@mgh.harvard.edu Sent: Wednesday, March 20, 2024 11:27 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu mailto: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?
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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Thanks Michael! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rullmann, Michael Michael.Rullmann@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-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 WONG Wan Wa <angelwong@ust.hkmailto:angelwong@ust.hk> Sent: Friday, April 5, 2024 12:14 PM To: Freesurfer support list <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?
External Email - Use Caution
Any idea about the PSF?
________________________________
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 WONG Wan Wa <angelwong@ust.hkmailto:angelwong@ust.hk> Sent: Tuesday, April 2, 2024 12:36 PM To: Freesurfer support list <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?
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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.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: Saturday, March 30, 2024 5:23 AM 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?
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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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of WONG Wan Wa angelwong@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?
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Thanks Michael! ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rullmann, Michael Michael.Rullmann@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:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1QhqrvAvEoqm5LPwY4Zobyu2ikbwoP-wu6qcl0XecyA4TLw...https://secure-web.cisco.com/1XqX9-a2LU-Yqo_eubkdqqmahVQPBMg1MvLiOSxV5SHgUNoohax6i_xqsuxgNWaGaYEFJOxJsV11MLT6HHPiItNJeCGcOpVrw3hkNph4i7cDnF6mIPBYXYS_7UwBKXePxqIoeUnn502yqPymKl-jCG3IF8rs4QJ23ue3hl1wCnMbVuMOqrbLmfa5WYv5SNbb9oJgRSyufzcncChaZUVs3DVHDzh_jFTwhKsxhutEHCAMvsT8v5R66-1qPhIKS_Y36ul2LwJnGJl5TNlrFnilUI5NJsunm5q7r9WSLf6AlvdPgxeuprMIa2pTRRORkGG3w/https%3A%2F%2Fwww.google.com%2Fsearch%3Fq%3Dnema%2Bfwhm%2Bsiemens%2BmMR
Second result links directly to the Siemens website:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1vR310-IMpTNOILEHO9JHWbD7YqwaQJjTYWwPbGET_p-STV...https://secure-web.cisco.com/1nbS9Vytnf798M-69hNgHUf9LyYJC4rkYI4w5c0QOt-Xd4n6mwlq-btGz5Nj6v4ciYO_m8LlBQQmPrMl26Bs9lG3WStwV-7GPVAEy2ABiy2zfNI3I5OvfjkMHzooOZUki5sPe70e6vm9lnb51h06HiA5lDgoO13QgqMhiNFRuUZoRp9usrCq8-ewf48IariB6LLxHlZyS_3jiTYj9KtBx_v6vfDFLq3M8hsUxnj2ar-P46i2JcRsfMLIUJQXlTCyTB0lp3-DbVtYFhsa6nvALJmqd3uEhHoM8B1VGbT5p9jT3FoMvds59LWkwoi0nHslf/https%3A%2F%2Fwww.siemens-healthineers.com%2Fmagnetic-resonance-imaging%2Fmr-pet-scanner%2Fbiograph-mmr
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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?
WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist.
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How to determine the PSF?
________________________________
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 WONG Wan Wa <angelwong@ust.hkmailto:angelwong@ust.hk> Sent: Friday, April 5, 2024 12:14 PM To: Freesurfer support list <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?
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Any idea about the PSF?
________________________________
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 WONG Wan Wa <angelwong@ust.hkmailto:angelwong@ust.hk> Sent: Tuesday, April 2, 2024 12:36 PM To: Freesurfer support list <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?
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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.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: Saturday, March 30, 2024 5:23 AM 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?
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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Douglas N. Greve -
Rullmann, Michael -
WONG Wan Wa