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

2024-04-11 Thread WONG Wan Wa 
External Email - Use Caution

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 
 on behalf of WONG Wan Wa 

Sent: Wednesday, April 10, 2024 5:16 PM
To: Freesurfer support list 
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 
 on behalf of Rullmann, Michael 

Sent: Tuesday, April 9, 2024 7:27 PM
To: Freesurfer support list 
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-wu6qcl0XecyA4TLwDHsnZn146qFvDNeQn3jb-qmiMMnVaOaSeKR-rSNIOmh1VWLJBCMPakN6yIeSE3Zmdq7aW17YgDcuMhin8DtSZypV8GYRGmKyISvwEiCDyzpmnjpLG2CC1KKGyvKiFgnxUdhc04exFYPgIdEz3xjPf-HxPNki64sl24TI9Jj3iu7DnCxTQsSoiMv3sMzSRuMSdNCNBBaQ88693Rcxm2twJRHQo-KKzOXray7lTKc-QQER8msZNOPOc_sP8hvb_snHS6esi2_TvUWikqokdrYD_NYXO6G_2M2G5qVjE_MQ/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-STVR95RchffDUVIZklZFP4ZbwQnBzQOCX_wr1vFg9jRAGV2Ipc9y6Z2Mmekz6R4Nq1371Otbhww7zMaWR0VXGGFjYu8dxo3aI1m5ox5RNFvUXuPWvOnQkLAdes0Y4t8Jll0JSc2HUUN3a3RB0x7fc5KGPsHX8-k3A4k2QXQK91TVEW9myjDcKf54VLFGCAqpOgsiCWczDgRwUeO-zrGnvV1w4_LusAVhY1xWcbX8kLtkFbb258tceZ4R66FcgzrGXp_-m3YjPqR-a1AX6G-DcatxMgP3zGlqS6EqkyeD6oA/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-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von WONG Wan Wa
Gesendet: Dienstag, 9. April 2024 12:03
An: Freesurfer support list 
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.



External Email - Use Caution

How to determine the PSF?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of WONG Wan Wa mailto:angelw...@ust.hk>>
Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list 
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>>
 on behalf of WONG Wan Wa mailto:angelw...@ust.hk>>
Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list 
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

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

2024-04-10 Thread WONG Wan Wa 
External Email - Use Caution

Thanks Michael!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rullmann, Michael 

Sent: Tuesday, April 9, 2024 7:27 PM
To: Freesurfer support list 
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/17cDaL3sO0H4g6J0do2HQsgfGNVcDVIz9kD4PAmCaVTEWsMF8cDN387a9bn7ZM0eHNz4e3PfSzVnPjmeZa5OfOr1nMzY_nZLfGZ2xixTpnxM3MqGSgL3D5uB_iqcLiIlg3XoM0WE43I29jjac3_I8BLA6J7usFOunC4FZbqb-yIyIaDH9Yvkl3eIbtqe-9XLGhd5gtqNnvsItOBuEQelSlJKoFutxvep8WE5UGugQZ4YNRVmoFsmnvLMtZptBWSOip2B-E700aNdpiKqu9KCpgiK_FTS9NaGOqnRa_hpZ_jMtt00QGAnFfORooGyZJJlIRpXByePuy0e2vroXi98cdg/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/1S0HAIGFEpyC5mVAakwzBOHaPqpZpfcqbi03UsYF4ZZfScXwF2YHko0qjR3IjdkGh1Sz2Q3i8AdCaLd1PwMtOxifeGNzw1kNJWPoS-W2vx8nDoR6hBKW0uhPnGl1NCDA4VrqCKRkKFrlnRaaFajJlIqy6_p_0lBBcpBVBccPCjgkYD-QPluq_J_Y2pu__js6Sef_5w0614u9u6jHj_CxlGX_8ax0Yk2oilVrfF7sYKrWY9fSvxwOrOve0kTTrn7o4xnGtWyj6c3MnXOPwzaIupi7ST0VfX3oMma_XJLS4_14oRIE7w7boN6QdGluW1VjXmZENRbpzSZWIUB7miIAe0w/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-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von WONG Wan Wa
Gesendet: Dienstag, 9. April 2024 12:03
An: Freesurfer support list 
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.



External Email - Use Caution

How to determine the PSF?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of WONG Wan Wa mailto:angelw...@ust.hk>>
Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list 
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>>
 on behalf of WONG Wan Wa mailto:angelw...@ust.hk>>
Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list 
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

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

2024-04-09 Thread Rullmann, Michael 
You can just google those values for each scanner.

For example:

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:

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-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von WONG Wan Wa
Gesendet: Dienstag, 9. April 2024 12:03
An: Freesurfer support list 
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. 

 

External Email - Use Caution

How to determine the PSF?

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of WONG Wan Wa 
mailto:angelw...@ust.hk> >
Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list 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> > on behalf of WONG Wan Wa 
mailto:angelw...@ust.hk> >
Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list 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-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Douglas N. Greve 
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> >
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 
   
 
 on behalf

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

2024-04-09 Thread WONG Wan Wa 
External Email - Use Caution

How to determine the PSF?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of WONG Wan Wa 

Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list 
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 
 on behalf of WONG Wan Wa 

Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list 
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 
 on behalf of Douglas N. Greve 

Sent: Saturday, March 30, 2024 5:23 AM
To: 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
 

 on behalf of Douglas N. Greve 

Sent: Thursday, March 21, 2024 9:44 PM
To: 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
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, March 20, 2024 11:27 PM
To: 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

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

2024-04-04 Thread WONG Wan Wa 
External Email - Use Caution

Any idea about the PSF?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of WONG Wan Wa 

Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list 
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 
 on behalf of Douglas N. Greve 

Sent: Saturday, March 30, 2024 5:23 AM
To: 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
 

 on behalf of Douglas N. Greve 

Sent: Thursday, March 21, 2024 9:44 PM
To: 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
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, March 20, 2024 11:27 PM
To: 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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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

2024-04-01 Thread WONG Wan Wa 
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 
 on behalf of Douglas N. Greve 

Sent: Saturday, March 30, 2024 5:23 AM
To: 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
 

 on behalf of Douglas N. Greve 

Sent: Thursday, March 21, 2024 9:44 PM
To: 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
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, March 20, 2024 11:27 PM
To: 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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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

2024-03-29 Thread Douglas N. Greve 
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 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, March 21, 2024 9:44 PM
*To:* 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 
 
 
 on behalf of Douglas 
N. Greve  

*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* 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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The information in this

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

2024-03-21 Thread WONG Wan Wa 
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 
 on behalf of Douglas N. Greve 

Sent: Thursday, March 21, 2024 9:44 PM
To: 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
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, March 20, 2024 11:27 PM
To: 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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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

2024-03-21 Thread Douglas N. Greve 
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 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, March 20, 2024 11:27 PM
*To:* 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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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

2024-03-20 Thread WONG Wan Wa 
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 
 on behalf of Douglas N. Greve 

Sent: Wednesday, March 20, 2024 11:27 PM
To: 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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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

2024-03-20 Thread Douglas N. Greve 
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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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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