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

[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<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-STVR95RchffDUVIZklZFP4ZbwQnBzQOCX_wr1vFg9jRAGV2Ipc9y6Z2Mmekz6R4Nq1371Otbhww7zMaWR0VXGGFjYu8dxo3aI1m5ox5RNFvUXuPWvOnQkLAdes0Y4t8Jll0JSc2HUUN3a3RB0x7fc5KGPsHX8-k3A4k2QXQK91TVEW9myjDcKf54VLFGCAqpOgsiCWczDgRwUeO-zrGnvV1w4_LusAVhY1xWcbX8kLtkFbb258tceZ4R66FcgzrGXp_-m3YjPqR-a1AX6G-DcatxMgP3zGlqS6EqkyeD6oA/https%3A%2F%2Fwww.siemens-healthineers.com%2Fmagnetic-resonance-imaging%2Fmr-pet-scanner%2Fbiograph-mmr<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>
 
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>
 
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 (ult

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

[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<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/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<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>
 
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>
 
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

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

[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>  
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>  
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>  
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>  
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

 

  _  

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

[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<mailto: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: 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>
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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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:

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

[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<mailto: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: 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>
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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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:Fr

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

[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<mailto: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: 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>
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>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<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> 
<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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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[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 
<mailto: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:* 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>
*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?

[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<mailto: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: 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>
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?

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

[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?

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

[WONG Wan Wa]

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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 .
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Re: [Freesurfer] PETSurfer

[Douglas N. Greve]

Hi, sorry for the many months to get back to you. I have just updated 
the documentation on https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
to indicate how to use your own segmentations. I'm assuming that you 
have a volume with choroid plexus labeled that you want  to merge into 
the stream. Take a look and see if that does what  you want.


On 9/26/2023 2:42 PM, Emma Tinney wrote:


External Email - Use Caution

Hi

I am reaching out to ask some questions about PetSurfer. I am working 
with an open access dataset (ADNIDOD 
) 
to analyze neurobiological differences in veterans with a history of 
TBI. I am hoping to use the PET data (there are the raw dicoms and 
preprocessed PET data) to segment the choroid plexus using aspecific 
segmentation software. 
I 
have already done the segmentation on the T1 images, but am hoping to 
apply the masks to the preprocessed PET images. I was looking at using 
the “mri_gtmpvc” command to segment the choroid plexus using the mask 
I already created but was hoping for some guidance.


There are also several options of preprocessed PET data I can chose 
from, including “co-registered averaged standardized image and voxel” 
including “co-registered averaged standardized image and voxel with 
unform resolution” and “co-registered averaged” or “co-registered 
dynamic”.


If anyone are willing to help or can connect me to someone how might 
have time to reply or quickly chat, that would be great. I appreciate 
the support and am looking forward to using PetSurfer.



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 .
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Re: [Freesurfer] PETsurfer kinetic modeling

[Douglas N. Greve]

There is not an easy way to do this yet. If you have your segmentations 
in the conformed anatomical space, you can merge them with gtmseg.mgz 
with something like
mri_vol2vol --interp nearest --mov yoursegs.mgz --targ gtmseg.mgz --o 
yoursegs-in-gtmseg-space.mgz
mergeseg --src gtmseg.mgz --merge yoursegs-in-gtmseg-space.mgz --o 
gtmseg+yoursegs.mgz
You will then need to copy gtmseg.ctab to gtmseg+yoursegs.ctab and edit 
it to include your new segs. Note that your new seg numbers should not 
overlap with anything in gtmseg. Once you create the new ctab, you can 
just copy it to other subjects.

Finally, copy gtmseg.lta to gtmseg+yoursegs.lta
Then run mri_gtmpvc passing --seg gtmseg+yoursegs.mgz

On 10/29/2023 1:21 PM, Dawn Matthews wrote:


External Email - Use Caution

Congratulations to the FreeSurfer team in the continued progress made 
in the FS tool set.  I wondered if you could comment on whether it is 
feasible to create a custom reference region (other than specifying, 
for example, cerebellar cortex or another predefined FS mask) for 
PETsurfer kinetic modeling (e.g. a cerebellum subfield) or whether 
there perhaps is an existing cerebellar subfield atlas that can be run 
with PETSurfer (e.g. crus2)?  In addition, can you please confirm 
whether the Logan model can be run using a reference region (i.e. 
without requiring arterial input)?  Thanks very much and kind regards.



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[Freesurfer] PETsurfer kinetic modeling

[Dawn Matthews]

External Email - Use Caution

Congratulations to the FreeSurfer team in the continued progress made in the FS 
tool set.  I wondered if you could comment on whether it is feasible to create 
a custom reference region (other than specifying, for example, cerebellar 
cortex or another predefined FS mask) for PETsurfer kinetic modeling (e.g. a 
cerebellum subfield) or whether there perhaps is an existing cerebellar 
subfield atlas that can be run with PETSurfer (e.g. crus2)?  In addition, can 
you please confirm whether the Logan model can be run using a reference region 
(i.e. without requiring arterial input)?  Thanks very much and kind regards.
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continue to communicate over unencrypted e-mail. 

[Freesurfer] PETSurfer

[Emma Tinney]

External Email - Use Caution

Hi

I am reaching out to ask some questions about PetSurfer. I am working with an 
open access dataset 
(ADNIDOD)
 to analyze neurobiological differences in veterans with a history of TBI. I am 
hoping to use the PET data (there are the raw dicoms and preprocessed PET data) 
to segment the choroid plexus using a specific segmentation 
software.
 I have already done the segmentation on the T1 images, but am hoping to apply 
the masks to the preprocessed PET images. I was looking at using the 
“mri_gtmpvc” command to segment the choroid plexus using the mask I already 
created but was hoping for some guidance.

There are also several options of preprocessed PET data I can chose from, 
including “co-registered averaged standardized image and voxel” including 
“co-registered averaged standardized image and voxel with unform resolution” 
and “co-registered averaged” or “co-registered dynamic”.

If anyone are willing to help or can connect me to someone how might have time 
to reply or quickly chat, that would be great. I appreciate the support and am 
looking forward to using PetSurfer.



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Re: [Freesurfer] PetSurfer, PET data format, mri_convert

[Wighton, Paul]

External Email - Use Caution

Hi Zeyu,

It looks like your files are in 'interfile' format.

If you have access to pmod, you might be able to use that to convert your files 
to nifti.
https://secure-web.cisco.com/1zqVVdVIc7totHjAN-r1V2oHpo0YeUbAKoFLyEzf5hGF_2QpNKUkYjapa61k7l3PSjeARv8qdfQNsmsWgyLM_x7yRo7uvps9iIp9uwO7a2TINpqT1lUcfZcSARBl8Fns-rGgqjVdinmxYTRRJW7qEhjB7TFy_Akeg1X6PozmQwtUClLKAap1CgLy0N6P-i1td6Epv8GJIS-_NewalfMvYf-uyOe7TemfME6k238__pKMda6B1y1hwLdR5PEBewmHUOTI5Z0xkuVuplriFkvuAaw/https%3A%2F%2Fwww.pmod.com%2Ffiles%2Fdownload%2Fv31%2Fdoc%2Fpbas%2F684.htm%23%3A%7E%3Atext%3DInterfile%2520is%2520a%2520file%2520format,version%203.3%2C%20Nucl%20Med%20Commun.

Or you could try using this: 
https://secure-web.cisco.com/1V87W-pEHHar2tKNTfSutV2rBhxv4QVhkEBhm-a5RZ9q6Gz-7E2XdigrjJkwDqcX7klh7tFuRWLL-91eC6kvPzjRRqZhQnS5wwjEH2gT566KrsPTsUSgBpXi1HnBlucbgC5JunCkl-6FVnKsvzu3cCbBMp82g0-NeCBdJM_xFIERvYEYDp6ArkE6kKJ18zQhGHc3KX4095fGBoZgt7_PI5_RP7B5AEA-HCHemz72hJe_7FTpJkw6Giy3l28FBafW09nazM9MZx3-XJ1nWYzDVRA/https%3A%2F%2Fgithub.com%2Frordenlab%2Fi2nii

Good luck!

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zhou, Zeyu 

Sent: Friday, July 28, 2023 10:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] PetSurfer, PET data format, mri_convert

External Email - Use Caution

Hi Freesurfer developers,

I am new to PET and FreeSurfer. I am trying to go through the PetSurfer 
tutorial (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1WIdRjlXspzVNAAubGnxONoOi-JQqlKFaZgFpmpGW_4cj_NGoWMbZCmxAW1Lx2XUGPrto07cKnoNmWSMabwUBhdizuJ3mimj9Xd_MWpUSafdFT4ojOiEHnwrT0iBPizzRaKXMlYsvKENtDO5ccRa8UEo9gWeMyQ0bNS2k2tUOQgdDchNUPKBRvJq54IaFi4y0eKS3ZSLgf78xNoL7Ng6qOqEMXMWX71tcHgARz3rerCE6795uAmZuqzjgij7h-thEDV9w3pPcJD-2qnuXbJpekQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer<https://secure-web.cisco.com/1SgXjbJz8ibehnENjVYIj14hM83pSJC3l0yNLV0Ubo9CVpoRewK5OxES53m1g56UEZ-L0ETzo4Rc8IsDydiXIeeWmtig-JVTf38MrXJgEig7jBCmIH1m-rCOdppmfFR5wfgg1_moJvMlaGmh_k1ETKxXWg2Wacf0cZvhVYuR5DFR1BJXYCAXEtP7FsfLzyU1CzhIPaI_b5kMDFt1eR8x60qTqr2FUBBzv_u8-A5VIvRrR-59G_W4Aac7OxqLCUzVxEYoa18Z0bBEgjXS-hCBj12Hv8QQmoyM5U0sU9HZrh0U40Wqke505AyMtqaJUm9EXuWiDjKfFEkEzXAenqlKtQA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>).
 In Part 4 "Reg
 ister your PET image with the anatomical", the PET data format in example is 
.nii.gz. However, here are the PET data I have (collected from SIEMENS HRRT 
PET):

309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i.hdr

I tried converting the .i file to (for example) an .nii file by mri_convert but 
got the following error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally0.nii
ERROR: cannot determine file type for 
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i

Then I changed the .i file's extension to .img and the .i.hdr file's extension 
to .hdr and run mri_convert, but still got an error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img 309Fally0.nii
reading from 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img...
error: ReadAnalyzeHeader: unsupported data type 17741

I couldn't find anywhere about how to process PET data in .i and .i.hdr files. 
Any suggestions? I attached one .i.hdr file for your reference.


1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
2) Platform: macOS Ventura 13.4.1 (c)
3) uname -a: Darwin rad-rsch-pc85 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun  
8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 arm64


Thanks.

Best,
Zeyu Zhou


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[Freesurfer] PetSurfer, PET data format, mri_convert

[Zhou, Zeyu]

External Email - Use Caution

Hi Freesurfer developers,

I am new to PET and FreeSurfer. I am trying to go through the PetSurfer 
tutorial 
(https://secure-web.cisco.com/1SgXjbJz8ibehnENjVYIj14hM83pSJC3l0yNLV0Ubo9CVpoRewK5OxES53m1g56UEZ-L0ETzo4Rc8IsDydiXIeeWmtig-JVTf38MrXJgEig7jBCmIH1m-rCOdppmfFR5wfgg1_moJvMlaGmh_k1ETKxXWg2Wacf0cZvhVYuR5DFR1BJXYCAXEtP7FsfLzyU1CzhIPaI_b5kMDFt1eR8x60qTqr2FUBBzv_u8-A5VIvRrR-59G_W4Aac7OxqLCUzVxEYoa18Z0bBEgjXS-hCBj12Hv8QQmoyM5U0sU9HZrh0U40Wqke505AyMtqaJUm9EXuWiDjKfFEkEzXAenqlKtQA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer).
 In Part 4 "Register your PET image with the anatomical", the PET data format 
in example is .nii.gz. However, here are the PET data I have (collected from 
SIEMENS HRRT PET):

309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame1_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame2_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame3_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame4_3D.i.hdr
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i
309Fally-309Fally-2021.8.23.11.51.13_EM_frame5_3D.i.hdr

I tried converting the .i file to (for example) an .nii file by mri_convert but 
got the following error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i 309Fally0.nii
ERROR: cannot determine file type for 
309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i

Then I changed the .i file's extension to .img and the .i.hdr file's extension 
to .hdr and run mri_convert, but still got an error message:

mri_convert 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img 309Fally0.nii
reading from 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.img...
error: ReadAnalyzeHeader: unsupported data type 17741

I couldn't find anywhere about how to process PET data in .i and .i.hdr files. 
Any suggestions? I attached one .i.hdr file for your reference.


1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460
2) Platform: macOS Ventura 13.4.1 (c)
3) uname -a: Darwin rad-rsch-pc85 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun  
8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020 arm64


Thanks.

Best,
Zeyu Zhou


309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
Description: 309Fally-309Fally-2021.8.23.11.51.13_EM_frame0_3D.i.hdr
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[Freesurfer] PetSurfer analisis whit another atlas

[Matteo Parodi]

External Email - Use Caution

Good morning.

I try to use surfer analysis with another atas instead of the built-in one.
I have an atlas in nifti or mgz format.
I tried using it in gtmseg's --head option and it doesn't work, maybe due
to normalization issues but I'm not sure.

I tried to build the atlas with the utilities in
https://secure-web.cisco.com/1npKm2rw7ypoDV5y3qkt0Aa0W2d4IRkHhrWfsjK3gU03P87txBiwTy7-f7R3Rto3y8N4_kOf6u_P2Ug5TIzjgW9Kyz2yg_Xrx9GHmtls2ihRa9A6dJjEQdGWN7_L7_WXDJdMVxU1o_U7GUNPPQFrNpRvkCssaHmzZg9f1TAR70VDfyflokv9qBa8mkG6u54awC-cX32YWUu-KDEXfUAivwXhe9WEbEYA0Cz5LslDpk-8_dqp6PA3st5GvNh7hQMRww3ztKpvAkkK6zUtsDZpBxLm3mVbeRx3TX7P4RFo1AggomqMJWCwXWcxZl1iM3sS8_-H2_yQvTQOE_KNVTuHzRw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCorticalParcellation
but i have problems to interfacing whit gca, gcs and annot file.

I searched the mail archive and found no answer.
Thank you very much for any input,
Parodi.
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Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

[Douglas N. Greve]

   External Email - Use Caution

what is the justification for using half that? 7.3 is not high in 
general. what scanner are you using?


On 5/8/2023 4:27 AM, Federica Di Antonio wrote:


External Email - Use Caution

Dear experts,
I am here again because I'd like to  ask a specification about the 
fwhm that the alghoritm evaluates: the main value that I obtained was 
7.3 mm; It is an high value for a pv correction.

May I put in half the value?
Because I wonder if the definition of fwhm used by mri_gtmpvc was 
different from mine.


Thenk you so much for your availability,

Federica Di Antonio

Il giorno lun 27 feb 2023 alle ore 14:30 Federica Di Antonio 
 ha scritto:


Thank you so much!



Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve
 ha scritto:

I have something called the adaptive GTM that is currently a
"hidden" feature in mri_gtmpvc as it has not been published
yet. You can try it by adding the following flags --opt 1
--opt-tol 4 10e-6 .02 --opt-seg-merge
When this is done, there will be a file called
gtmdir/aux/opt.params.dat The value in that file with be the
fwhm. Run mri_gtmpvc again passing that value as the --psf
Again, this has not been fully evaluated so use at your own risk.


On 12/12/2022 3:10 AM, Federica Di Antonio wrote:


External Email - Use Caution

Dear experts,

Few weeks ago i wrote to this mailing list but I didn't
receive any answer, so I'll try again:


mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg 
gtmseg.mgz
  --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output


If I put psf to 0, there is no PVC, and the same happens if I don’t put 
that flag at all.t all

Is able mri_gtmpvc to evaluate the fwhm without receiving it from the 
user?
I apologize for the repetition,
Thanks for your patience,
Federica

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Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

[Federica Di Antonio]

External Email - Use Caution

Dear experts,
I am here again because I'd like to  ask a specification about the fwhm
that the alghoritm evaluates: the main value that I obtained was 7.3 mm; It
is an high value for a pv correction.
May I put in half the value?
Because I wonder if the definition of fwhm used by mri_gtmpvc was different
from mine.

Thenk you so much for your availability,

Federica Di Antonio

Il giorno lun 27 feb 2023 alle ore 14:30 Federica Di Antonio <
fedediantoni...@gmail.com> ha scritto:

> Thank you so much!
>
>
>
> Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve <
> dgr...@mgh.harvard.edu> ha scritto:
>
>> I have something called the adaptive GTM that is currently a "hidden"
>> feature in mri_gtmpvc as it has not been published yet. You can try it by
>> adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge
>> When this is done, there will be a file called gtmdir/aux/opt.params.dat
>> The value in that file with be the fwhm. Run mri_gtmpvc again passing that
>> value as the --psf
>> Again, this has not been fully evaluated so use at your own risk.
>>
>>
>> On 12/12/2022 3:10 AM, Federica Di Antonio wrote:
>>
>> External Email - Use Caution
>>
>> Dear experts,
>>
>>
>>
>> Few weeks ago i wrote to this mailing list but I didn't receive any
>> answer, so I'll try again:
>>
>>
>> mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
>>
>>  --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output
>>
>>
>> If I put psf to 0, there is no PVC, and the same happens if I don’t put that 
>> flag at all.t all
>>
>> Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?
>>
>> I apologize for the repetition,
>>
>> Thanks for your patience,
>>
>> Federica
>>
>>
>> ___
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>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>> 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
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>>  <
>> https://secure-web.cisco.com/1TZZ5-LguqY1kjLdVWbgRzIIMt1eUtKCc0bCXQn4iNu-CguFeOzu8AcxkD3DqkROwVR8TSv5pnOW7GGs7RWj9gQz7VnvsMXNfHQEaLcyFrsDwBaSkIs4o0mEuuqOJ-juazmgvtvgO9Yi67suKeP0gp6v6xdjY47XS6IM1vdXCcFxigDJObdp-UOu1CXiEPGj95bWlnveSUwJGAOBrMfPjzHv3tOKH_BOVj14blt3ekk1qwI3pt4Ma0Va05k8zdYqD-Zum2SP4xUoSWgg1tmPpW4vMznpi-Q6pjtUnKuSSXTbSLAAG_HN0oFCV0XVD2VwvkL16SWnDXK2ZXadLhlNShQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
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[Freesurfer] PETsurfer registration

[Douglas N. Greve]

On the PETsurfer wiki, 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer, I had recommended 
using mri_coreg to register your PET to the FS anatomical using the 
following command line:

mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta

This works well for PET scans that do not have much activity outside the 
head (eg, FDG and many neuroreceptor ligands). However, it can be 
inaccurate for other ligands that do have lots of uptake outside the 
head (eg, tspo, maybe tau). In these cases I now recommend using

mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta --ref 
nu.mgz --no-ref-mask

This command will use the whole head MRI (nu.mgz) instead of the 
brainmasked MRI (brainmask.mgz); this will align better for these types 
of scans. This is now documented on the PETsurfer website.

Remember, you should always check your PET-MR registrations manually.

Sorry for any inconvenience this has created.

best
doug


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Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

[Federica Di Antonio]

External Email - Use Caution

Thank you so much!



Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:

> I have something called the adaptive GTM that is currently a "hidden"
> feature in mri_gtmpvc as it has not been published yet. You can try it by
> adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge
> When this is done, there will be a file called gtmdir/aux/opt.params.dat
> The value in that file with be the fwhm. Run mri_gtmpvc again passing that
> value as the --psf
> Again, this has not been fully evaluated so use at your own risk.
>
>
> On 12/12/2022 3:10 AM, Federica Di Antonio wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
>
>
> Few weeks ago i wrote to this mailing list but I didn't receive any
> answer, so I'll try again:
>
>
> mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
>
>  --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output
>
>
> If I put psf to 0, there is no PVC, and the same happens if I don’t put that 
> flag at all.t all
>
> Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?
>
> I apologize for the repetition,
>
> Thanks for your patience,
>
> Federica
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
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> e-mail contains patient information, please contact the Mass General
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>  .
>
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Re: [Freesurfer] PetSurfer - MG coregister

[Douglas N. Greve]

When you load it into freeview, use the aux/bbpet2anat.lta , eg,
freeview orig.mgz aseg.mgz mgx.ctxgm.nii.gz:reg=aux/bbpet2anat.lta


On 1/17/2023 12:46 PM, Marina Fernández wrote:


External Email - Use Caution

Dear experts,

I am trying to do PVC on FBB-PET images using the following commands:

"
mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg 
s_001_pet_fbb.reg.lta


mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 
6 --seg gtmseg.mgz --rescale 174 --default-seg-merge  --auto-mask  
--mgx .1 --o s_001_pet_fbb

"

The problem is that when overlaying the mgx.ctxgm.nii.gz file with the 
T1.mgz of the corresponding subject, they don't match, since the 
resulting MG-image is in the space of the original PET (without PVC) 
instead of in the space of the freesurfer subject.


How can I make the MG image be in the freesurfer's subject space? 
Where is the error?

Thank you very much in advance.

Best regards,
Marina

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Re: [Freesurfer] PetSurfer - MG coregister

[Rahul Sharma]

External Email - Use Caution

Thank you so much. Now I at least get a direction from where to start.

Regards:
Rahul Sharma
Research Scholar
NIT Silchar
Assam
9827834360


*"Manners Maketh Man"*



On Wed, Jan 18, 2023 at 5:36 PM Marina Fernández <
marina.fdez.alva...@gmail.com> wrote:

> External Email - Use Caution
>
> Dear Rahul,
>
> I just used the wiki of the Freesurfer functions, the information is very
> complete. If you want to use Freesurfer, you can start by doing the
> cortical reconstruction process for each subject (*MailScanner has
> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
> be* 
> https://secure-web.cisco.com/1wNUHXriYjbVu0pnP9lPibBpSibvic3FYCGXOkzHJJYUyEy0s8QzZZy8cEMzn-7VDkwtEcIbj5CrSHY6QvT--S1RzjgE2fxiIQM9_ys88ArF0BDVMjK6xd6rC3aSxrc9MpHHpGQ94hFpSkW9QWtgUMVijU_m1FMn8U7JVlce1m6PzO9JKIHWXVHD1w193tqD53HPwk3zcDixpx_Yhvf4VnyH2XmC_OleQkS4kYFj8AuUFk1iZzPmagrneIX1B7-F6y7hAYC1XKhe7IUi5uaLbvkClz5qB495PyknKHiMEQ0dtk_TL2LdKKzkQhn7h0kscQiOrpKGpstaTK_IpwB0D1Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all
> )
> and then prepare the maps to do the analysis that interests you. In the
> case of PET analysis, you can follow the steps explained on the PetSurfer
> wiki (*MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1Q8C3MaQsBXeeptNwjLzLRUZeefaYoz5wdGthwLyZKQcjQX8pV6ep29iW0U7qw83lpdNG0wesOlzytDKDm34YBEu64e6bCznE2Da0LxzZPjCuiXPNamIt9lXeeB3RdANHvCNRJT4XQpBTvS8LeUvBFUlvGQebzPE2zrS_xqzkpRlroAEpX7xumPpZ7mVSUFPioryJBXvfwgYdKTnuSdoUHxXT1HFf8oI2fpYWBt6_qhIrq_D4XKctZy-wi7ZCJwXzPxrKDy2MI7QK-fkn0y62q7baQEU84z3xLLGk27eOI5xkVNAk8jvEhSHXm0_0Fx-POLA_z_AY1KHMJODEihEkJQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
> ).
> If you have any particular questions about feature options, you can search
> this list if other users have asked before. In case the question is not
> resolved, you can ask it here so that the experts can answer you.
>
> I hope it helps.
>
> Cheers,
>
> Marina.
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>  .
>
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Re: [Freesurfer] PetSurfer - MG coregister

[Marina Fernández]

External Email - Use Caution

Dear Rahul,

I just used the wiki of the Freesurfer functions, the information is very
complete. If you want to use Freesurfer, you can start by doing the
cortical reconstruction process for each subject (
https://secure-web.cisco.com/1Lj_XzmtE_iAYreTtmjwq2Q0VTCaZWdcX4QFapQPQO_Y7jt5UUJInKYqrNhnXGwnk1sLb7wJq2Wh3qysFyE7A2vatYoHcPHMZHo7GYENuDlLem9W0-2BYIamTvvCFMLLdCUnxLU_G7Cxt88FHc7rc9SBSXeNFKxnmcE92mDpGq17kkG7e5z1xxHMzZ3qqP3i3PsGWTuJ6iXrcCjxYWeUhyFKY-4sYocBxCbnGhmtklucq_krPXq_4UJxnqM4r9GRbforAUguSKj5gWmdJM1j2aenoUDAnZ8cJD7FDo8lzUrrdw-V0NiaO0QpgQu0IuT31aquJZ0ozRGVWMjncSaL6_g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all)
 and then prepare the
maps to do the analysis that interests you. In the case of PET analysis,
you can follow the steps explained on the PetSurfer wiki (
https://secure-web.cisco.com/1SUsUq0XwDtpjwx2dSpE1KOdwDPRl2MG5fyhegdBeDHaK3Kus53Dl6TsyWNEAmQYkn3zf_z62wLaf9lukg3fVOx19cKVvlp-3v3YJWc3n5olJg5s58sSDWVl30wlU6zsBXAQTPs5T4sbeal0Emw9SBV5Rm6WNIfFZ6YRqbQISso9Qaa-CZMD4fKaiP6VNNEYJyAT5OMcGS3C7yfEz9pqobDPA9nbmXH4hTxnURBQjj7_w4ViNBDGceVs6u7qpGUUI7-BBcn1ilRhAM33-kZF3Wmf3EslOFVPXhw8BZD5CPBoHh2Koriy242CdL90U-fp3-SVsHmj4TLz6889vBVOaVQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer).
 If you have any
particular questions about feature options, you can search this list if
other users have asked before. In case the question is not resolved, you
can ask it here so that the experts can answer you.

I hope it helps.

Cheers,

Marina.
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Re: [Freesurfer] PetSurfer - MG coregister

[Rahul Sharma]

External Email - Use Caution

Hello Mam,
I am not replying to your mail, instead I need to know the source where you
learn Freesurfer and pre processing of MRI and PET.
Please do reply.



On Tue, 17 Jan 2023, 11:16 pm Marina Fernández, <
marina.fdez.alva...@gmail.com> wrote:

> External Email - Use Caution
>
> Dear experts,
>
> I am trying to do PVC on FBB-PET images using the following commands:
>
> "
> mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta
>
> mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6
> --seg gtmseg.mgz --rescale 174 --default-seg-merge  --auto-mask  --mgx .1
> --o s_001_pet_fbb
> "
>
> The problem is that when overlaying the mgx.ctxgm.nii.gz file with the
> T1.mgz of the corresponding subject, they don't match, since the resulting
> MG-image is in the space of the original PET (without PVC) instead of in
> the space of the freesurfer subject.
>
> How can I make the MG image be in the freesurfer's subject space? Where
> is the error?
> Thank you very much in advance.
>
> Best regards,
> Marina
> ___
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> e-mail contains patient information, please contact the Mass General
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>  <
> https://secure-web.cisco.com/1Y2n0Lt7qelLI-6JcOyuLSMDYPYuinaE5gMBud17DDwdaQZmyhfHkP_N_4jvdM-vlUTHc1epJoJes8ZCF44D2MoknTyRxX0M-frpquXzYxWm7VMRxqu6bjKcFjrYLviHX6DgyCoL7PZTf8XnPPlXCUhkzOtA08tHc-NKCte0t1r93twk-1OPL3J8P8Oft5Lqy7nCIMYfvqBLemr1wZqWD1TePa04YAMeI85TTCQRSxVJRZGTWbH2U2F_rabLuWdJK7ttYr114w4nOS2OIM2Q5JFCqZxAuILcjhOQGFJt63GA2eQmuVz_vkvjfecLx_8yN59LyECh99LSJh0LxQyXJyw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
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[Freesurfer] PetSurfer - MG coregister

[Marina Fernández]

External Email - Use Caution

Dear experts,

I am trying to do PVC on FBB-PET images using the following commands:

"
mri_coreg --s s_001 --mov s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta

mri_gtmpvc --i s_001_pet_fbb.nii.gz --reg s_001_pet_fbb.reg.lta --psf 6
--seg gtmseg.mgz --rescale 174 --default-seg-merge  --auto-mask  --mgx .1
--o s_001_pet_fbb
"

The problem is that when overlaying the mgx.ctxgm.nii.gz file with the
T1.mgz of the corresponding subject, they don't match, since the resulting
MG-image is in the space of the original PET (without PVC) instead of in
the space of the freesurfer subject.

How can I make the MG image be in the freesurfer's subject space? Where is
the error?
Thank you very much in advance.

Best regards,
Marina
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Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

[Douglas N. Greve]

I have something called the adaptive GTM that is currently a "hidden" 
feature in mri_gtmpvc as it has not been published yet. You can try it 
by adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge
When this is done, there will be a file called gtmdir/aux/opt.params.dat 
The value in that file with be the fwhm. Run mri_gtmpvc again passing 
that value as the --psf

Again, this has not been fully evaluated so use at your own risk.


On 12/12/2022 3:10 AM, Federica Di Antonio wrote:


External Email - Use Caution

Dear experts,

Few weeks ago i wrote to this mailing list but I didn't receive any 
answer, so I'll try again:



mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
  --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output


If I put psf to 0, there is no PVC, and the same happens if I don’t put that 
flag at all.t all

Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?
I apologize for the repetition,
Thanks for your patience,
Federica

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[Freesurfer] PETsurfer: PVC without psf of the scanner

[Federica Di Antonio]

External Email - Use Caution

Dear experts,



Few weeks ago i wrote to this mailing list but I didn't receive any answer,
so I'll try again:


mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz

 --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output


If I put psf to 0, there is no PVC, and the same happens if I don’t
put that flag at all.t all

Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?

I apologize for the repetition,

Thanks for your patience,


Federica
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[Freesurfer] PETsurfer: PVC without psf of the scanner

[Federica]

External Email - Use CautionDear experts,  mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output About this command, is there the possibility for PETsurfer to compute the fwhm of the psf of the scanner without being provided by the user?  If i put psf to 0, there is no PVC, and the same if I don’t put that flag at all. I wonder if PETsurfer is able to estimates fwhm by itself (doing something like the FWHM of smoothing  in step 8.2). I hope that my english is enough clear to be understood. Thank you so much for your kindness, best regards, Federica  Inviato da Posta per Windows 
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Re: [Freesurfer] PETSurfer tutorial images?

[Douglas N. Greve]

that's from a tutorial that I never finished. You can get the data from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/sb01.tar.gz
https://gate.nmr.mgh.harvard.edu/safelinks/greve/uw.fsf01anat.tar.gz
username guest
pwd collab


On 9/26/2022 12:13 PM, daedalu...@aol.com wrote:


External Email - Use Caution

Dear FreeSurfer/PETSurfer experts,
I am beginning to explore the functionality of PETSurfer, and in the 
Wiki there is reference to a set of 18 folders (" called s01, s02, 
etc"), and I am wondering if that dataset is publicly available (and 
if so, where?). I am particularly interested in an example of the 
format/layout of the file:
"frame.time.dat -- text file indicating the time at which each frame 
was acquired."
In order to test my syntax, it would be very useful to have a set of 
explicit volumes and text files.

Sincerely,
-Randy

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[Freesurfer] PETSurfer tutorial images?

[daedalus39]

External Email - Use Caution

Dear FreeSurfer/PETSurfer experts, I am beginning to explore the functionality 
of PETSurfer, and in the Wiki there is reference to a set of 18 folders (" 
called s01, s02, etc"), and I am wondering if that dataset is publicly 
available (and if so, where?).  I am particularly interested in an example of 
the format/layout of the file: "frame.time.dat -- text file indicating the time 
at which each frame was acquired." In order to test my syntax, it would be very 
useful to have a set of explicit volumes and text files. Sincerely, -Randy___
Freesurfer mailing list
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Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

yes, it does

On 2/25/2022 5:14 PM, Jennifer Bramen wrote:


External Email - Use Caution

Hi Doug

I want to confirm that the signal any region flagged as cortex is 
restricted to gray matter. If that is the case, then I finally have 
what I need. Thank you.


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Friday, February 25, 2022 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

Are you doing an ROI analysis or a voxel-wise analysis? If an ROI 
analysis, then use mri_gtmpvc (with or without PVC). This will give 
you GM, WM, and CSF ROIs. Or do you mean you want a single average 
across all GM?


On 2/24/2022 1:15 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I would like to measure uptake exclusively in gray matter. What
would you recommend to accomplish this?

In my previous message, I was wondering if adding a gray matter
mask would be a potential way to restrict the analysis to gray
matter. Thanks!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, February 22, 2022 at 3:00 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

    <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

I don't understand. What mask?

On 2/22/2022 8:55 AM, Jennifer Bramen wrote:

*External Email - Use Caution *

If I only want to extract intensity from gray matter, do I
need to add an additional mask?

Thanks!

Jennifer

Get Outlook for iOS

<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>



*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:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu
    
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: subcortical
volume-based analysis

The GTM gives you values for each ROI regardless of whether it
is GM, WM, or CSF. They will probably give you similar
answers, but the GTM will be more robust.

On 2/21/2022 8:48 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Thanks! Yes, I already mapped my PET to anatomical space
using mri_vol2vol and glmdir/aux/bbpet2anat.lta.

RE: selection of mgx instead of gtm: I am analyzing
amyloid PET data and I believe it is recommended to
extract gray matter localized PET data. Is that what I am
doing by using the mgx image?

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience
Institute & Foundation | Providence Saint John's Health
Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf
of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesur

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Jennifer Bramen]

External Email - Use Caution

Hi Doug

I want to confirm that the signal any region flagged as cortex is restricted to 
gray matter. If that is the case, then I finally have what I need. Thank you.

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Friday, February 25, 2022 at 10:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

Are you doing an ROI analysis or a voxel-wise analysis? If an ROI analysis, 
then use mri_gtmpvc (with or without PVC). This will give you GM, WM, and CSF 
ROIs. Or do you mean you want a single average across all GM?
On 2/24/2022 1:15 PM, Jennifer Bramen wrote:

External Email - Use Caution

I would like to measure uptake exclusively in gray matter. What would you 
recommend to accomplish this?
In my previous message, I was wondering if adding a gray matter mask would be a 
potential way to restrict the analysis to gray matter. Thanks!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069



From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, February 22, 2022 at 3:00 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

I don't understand. What mask?
On 2/22/2022 8:55 AM, Jennifer Bramen wrote:

External Email - Use Caution


If I only want to extract intensity from gray matter, do I need to add an 
additional mask?

Thanks!

Jennifer

Get Outlook for 
iOS<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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: Monday, February 21, 2022 7:13:39 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

The GTM gives you values for each ROI regardless of whether it is GM, WM, or 
CSF. They will probably give you similar answers, but the GTM will be more 
robust.
On 2/21/2022 8:48 PM, Jennifer Bramen wrote:

External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and 
glmdir/aux/bbpet2anat.lta.



RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I 
believe it is recommended to extract gray matter localized PET data. Is that 
what I am doing by using the mgx image?



Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069







From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, February 21, 2022 at 2:02 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis



You need to first map your pet to the anatomical space using mri_vol2vol and 
the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead of using 
the output from the gtm? Note that you cannot use the white matter values that 
come from  mgx.

On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

E

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

Are you doing an ROI analysis or a voxel-wise analysis? If an ROI 
analysis, then use mri_gtmpvc (with or without PVC). This will give you 
GM, WM, and CSF ROIs. Or do you mean you want a single average across 
all GM?


On 2/24/2022 1:15 PM, Jennifer Bramen wrote:


External Email - Use Caution

I would like to measure uptake exclusively in gray matter. What would 
you recommend to accomplish this?


In my previous message, I was wondering if adding a gray matter mask 
would be a potential way to restrict the analysis to gray matter. Thanks!


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Tuesday, February 22, 2022 at 3:00 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

I don't understand. What mask?

On 2/22/2022 8:55 AM, Jennifer Bramen wrote:

*External Email - Use Caution *

If I only want to extract intensity from gray matter, do I need to
add an additional mask?

Thanks!

Jennifer

Get Outlook for iOS

<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>



*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:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

The GTM gives you values for each ROI regardless of whether it is
GM, WM, or CSF. They will probably give you similar answers, but
the GTM will be more robust.

On 2/21/2022 8:48 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Thanks! Yes, I already mapped my PET to anatomical space using
mri_vol2vol and glmdir/aux/bbpet2anat.lta.

RE: selection of mgx instead of gtm: I am analyzing amyloid
PET data and I believe it is recommended to extract gray
matter localized PET data. Is that what I am doing by using
the mgx image?

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
    
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical
volume-based analysis

You need to first map your pet to the anatomical space using
mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data
instead of using the output from the gtm? Note that you cannot
use the white matter values that come from  mgx.

On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I am trying to extract mean intensity in my PET data for
every ROI. Doug said to run mri_segstats passing the PET
with --i and using --seg to spec the segmentation.*I would
like to confirm that I am using this properly.*

mri_segstats --i
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel
lh --sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz
is the PET data regi

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Jennifer Bramen]

External Email - Use Caution


I would like to measure uptake exclusively in gray matter. What would you 
recommend to accomplish this?
In my previous message, I was wondering if adding a gray matter mask would be a 
potential way to restrict the analysis to gray matter. Thanks!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069



From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, February 22, 2022 at 3:00 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

I don't understand. What mask?
On 2/22/2022 8:55 AM, Jennifer Bramen wrote:

External Email - Use Caution


If I only want to extract intensity from gray matter, do I need to add an 
additional mask?

Thanks!

Jennifer

Get Outlook for 
iOS<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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: Monday, February 21, 2022 7:13:39 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

The GTM gives you values for each ROI regardless of whether it is GM, WM, or 
CSF. They will probably give you similar answers, but the GTM will be more 
robust.
On 2/21/2022 8:48 PM, Jennifer Bramen wrote:

External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and 
glmdir/aux/bbpet2anat.lta.



RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I 
believe it is recommended to extract gray matter localized PET data. Is that 
what I am doing by using the mgx image?



Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069







From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, February 21, 2022 at 2:02 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis



You need to first map your pet to the anatomical space using mri_vol2vol and 
the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead of using 
the output from the gtm? Note that you cannot use the white matter values that 
come from  mgx.

On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

External Email - Use Caution

I am trying to extract mean intensity in my PET data for every ROI. Doug said 
to run mri_segstats passing the PET with --i and using --seg to spec the 
segmentation. I would like to confirm that I am using this properly.



mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg 
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum 
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg



where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data 
registered and resampled into the individual’s T1-weighrd MRI space.







Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069





From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 16, 2022 at 7:30 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.ha

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

I don't understand. What mask?

On 2/22/2022 8:55 AM, Jennifer Bramen wrote:


External Email - Use Caution



If I only want to extract intensity from gray matter, do I need to add 
an additional mask?


Thanks!

Jennifer

Get Outlook for iOS 
<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
The GTM gives you values for each ROI regardless of whether it is GM, 
WM, or CSF. They will probably give you similar answers, but the GTM 
will be more robust.


On 2/21/2022 8:48 PM, Jennifer Bramen wrote:


External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using 
mri_vol2vol and glmdir/aux/bbpet2anat.lta.


RE: selection of mgx instead of gtm: I am analyzing amyloid PET data 
and I believe it is recommended to extract gray matter localized PET 
data. Is that what I am doing by using the mgx image?


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas 
N. Greve"  <mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list  
<mailto:freesurfer@nmr.mgh.harvard.edu>

*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

You need to first map your pet to the anatomical space using 
mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead 
of using the output from the gtm? Note that you cannot use the white 
matter values that come from mgx.


On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I am trying to extract mean intensity in my PET data for every
ROI. Doug said to run mri_segstats passing the PET with --i and
using --seg to spec the segmentation.*I would like to confirm
that I am using this properly.*

mri_segstats --i
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the
PET data registered and resampled into the individual’s
T1-weighrd MRI space.

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

If you want to do an ROI analysis using FS-based ROIs, you should
do that at the individual level. Resample the PET to the
anatoimical space, then run mri_segstats passing the PET with --i
and using --seg to spec the segmentation. If you really want to
do it in MNI305 space, then it is the same thing just using the
MNI305-based (2mm) segmentation

On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have
completed all of the steps from the PetSurfer wiki. I now
have the preprocessed, averaged, resampled, smoothed PET data
in MNI305 space whic

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Jennifer Bramen]

External Email - Use Caution


If I only want to extract intensity from gray matter, do I need to add an 
additional mask?

Thanks!

Jennifer

Get Outlook for 
iOS<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, February 21, 2022 7:13:39 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

The GTM gives you values for each ROI regardless of whether it is GM, WM, or 
CSF. They will probably give you similar answers, but the GTM will be more 
robust.

On 2/21/2022 8:48 PM, Jennifer Bramen wrote:

External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and 
glmdir/aux/bbpet2anat.lta.



RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I 
believe it is recommended to extract gray matter localized PET data. Is that 
what I am doing by using the mgx image?



Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069







From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, February 21, 2022 at 2:02 PM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis



You need to first map your pet to the anatomical space using mri_vol2vol and 
the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead of using 
the output from the gtm? Note that you cannot use the white matter values that 
come from  mgx.

On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

External Email - Use Caution

I am trying to extract mean intensity in my PET data for every ROI. Doug said 
to run mri_segstats passing the PET with --i and using --seg to spec the 
segmentation. I would like to confirm that I am using this properly.



mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg 
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum 
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg



where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data 
registered and resampled into the individual’s T1-weighrd MRI space.







Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069





From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 16, 2022 at 7:30 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis



If you want to do an ROI analysis using FS-based ROIs, you should do that at 
the individual level. Resample the PET to the anatoimical space, then run 
mri_segstats passing the PET with --i and using --seg to spec the segmentation. 
If you really want to do it in MNI305 space, then it is the same thing just 
using the MNI305-based (2mm) segmentation

On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

External Email - Use Caution

Dear Freesurfer Developers



I am doing an ROI--based amyloid PET scan analysis. I have completed all of the 
steps from the PetSurfer wiki. I now have the preprocessed, averaged, 
resampled, smoothed PET data in MNI305 space which is constrained to the 
subcortical gray matter mask.



How do I extract mean intensity within all of the subcortical ROI?



Thank you!



Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Pr

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

The GTM gives you values for each ROI regardless of whether it is GM, 
WM, or CSF. They will probably give you similar answers, but the GTM 
will be more robust.


On 2/21/2022 8:48 PM, Jennifer Bramen wrote:


External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using 
mri_vol2vol and glmdir/aux/bbpet2anat.lta.


RE: selection of mgx instead of gtm: I am analyzing amyloid PET data 
and I believe it is recommended to extract gray matter localized PET 
data. Is that what I am doing by using the mgx image?


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

You need to first map your pet to the anatomical space using 
mri_vol2vol and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead 
of using the output from the gtm? Note that you cannot use the white 
matter values that come from  mgx.


On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

I am trying to extract mean intensity in my PET data for every
ROI. Doug said to run mri_segstats passing the PET with --i and
using --seg to spec the segmentation.*I would like to confirm that
I am using this properly.*

mri_segstats --i
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the
PET data registered and resampled into the individual’s T1-weighrd
MRI space.

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>

    <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based
analysis

If you want to do an ROI analysis using FS-based ROIs, you should
do that at the individual level. Resample the PET to the
anatoimical space, then run mri_segstats passing the PET with --i
and using --seg to spec the segmentation. If you really want to do
it in MNI305 space, then it is the same thing just using the
MNI305-based (2mm) segmentation

On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have
completed all of the steps from the PetSurfer wiki. I now have
the preprocessed, averaged, resampled, smoothed PET data in
MNI305 space which is constrained to the subcortical gray
matter mask.

*How do I extract mean intensity within all of the subcortical
ROI?*

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069




___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Jennifer Bramen]

External Email - Use Caution

Thanks! Yes, I already mapped my PET to anatomical space using mri_vol2vol and 
glmdir/aux/bbpet2anat.lta.

RE: selection of mgx instead of gtm: I am analyzing amyloid PET data and I 
believe it is recommended to extract gray matter localized PET data. Is that 
what I am doing by using the mgx image?

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069



From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Monday, February 21, 2022 at 2:02 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

You need to first map your pet to the anatomical space using mri_vol2vol and 
the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead of using 
the output from the gtm? Note that you cannot use the white matter values that 
come from  mgx.
On 2/21/2022 12:57 PM, Jennifer Bramen wrote:

External Email - Use Caution
I am trying to extract mean intensity in my PET data for every ROI. Doug said 
to run mri_segstats passing the PET with --i and using --seg to spec the 
segmentation. I would like to confirm that I am using this properly.

mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg 
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum 
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data 
registered and resampled into the individual’s T1-weighrd MRI space.



Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 16, 2022 at 7:30 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

If you want to do an ROI analysis using FS-based ROIs, you should do that at 
the individual level. Resample the PET to the anatoimical space, then run 
mri_segstats passing the PET with --i and using --seg to spec the segmentation. 
If you really want to do it in MNI305 space, then it is the same thing just 
using the MNI305-based (2mm) segmentation
On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

External Email - Use Caution
Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have completed all of the 
steps from the PetSurfer wiki. I now have the preprocessed, averaged, 
resampled, smoothed PET data in MNI305 space which is constrained to the 
subcortical gray matter mask.

How do I extract mean intensity within all of the subcortical ROI?

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069






___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

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Freesurfer mailing l

Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

You need to first map your pet to the anatomical space using mri_vol2vol 
and the registration glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx data instead of 
using the output from the gtm? Note that you cannot use the white matter 
values that come from  mgx.


On 2/21/2022 12:57 PM, Jennifer Bramen wrote:


External Email - Use Caution

I am trying to extract mean intensity in my PET data for every ROI. 
Doug said to run mri_segstats passing the PET with --i and using --seg 
to spec the segmentation.*I would like to confirm that I am using this 
properly.*


mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz 
--seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh 
--sum $PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg


where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET 
data registered and resampled into the individual’s T1-weighrd MRI space.


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

If you want to do an ROI analysis using FS-based ROIs, you should do 
that at the individual level. Resample the PET to the anatoimical 
space, then run mri_segstats passing the PET with --i and using --seg 
to spec the segmentation. If you really want to do it in MNI305 space, 
then it is the same thing just using the MNI305-based (2mm) segmentation


On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

*External Email - Use Caution *

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have
completed all of the steps from the PetSurfer wiki. I now have the
preprocessed, averaged, resampled, smoothed PET data in MNI305
space which is constrained to the subcortical gray matter mask.

*How do I extract mean intensity within all of the subcortical ROI?*

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

*MailScanner has detected a possible fraud attempt from
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Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Jennifer Bramen]

External Email - Use Caution

I am trying to extract mean intensity in my PET data for every ROI. Doug said 
to run mri_segstats passing the PET with --i and using --seg to spec the 
segmentation. I would like to confirm that I am using this properly.

mri_segstats --i $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz --seg 
$SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh --slabel lh --sum 
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg

where $PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is the PET data 
registered and resampled into the individual’s T1-weighrd MRI space.



Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Wednesday, February 16, 2022 at 7:30 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

If you want to do an ROI analysis using FS-based ROIs, you should do that at 
the individual level. Resample the PET to the anatoimical space, then run 
mri_segstats passing the PET with --i and using --seg to spec the segmentation. 
If you really want to do it in MNI305 space, then it is the same thing just 
using the MNI305-based (2mm) segmentation
On 2/14/2022 6:11 PM, Jennifer Bramen wrote:

External Email - Use Caution
Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have completed all of the 
steps from the PetSurfer wiki. I now have the preprocessed, averaged, 
resampled, smoothed PET data in MNI305 space which is constrained to the 
subcortical gray matter mask.

How do I extract mean intensity within all of the subcortical ROI?

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069





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Re: [Freesurfer] PetSurfer: CORTICAL volume-based analysis

[Douglas N. Greve]

I just sent info on how to do this, but see step 5 in the wiki

On 2/14/2022 6:27 PM, Jennifer Bramen wrote:


External Email - Use Caution

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I am following the 
steps from the PetSurfer wiki. I see instructions for how to do a 
cortical surface-based group analysis. I also see how to do a 
subcortical ROI-based analysis. However, I cannot find detailed 
instructions for performing a cortical ROI-based analysis.


This is how I think I should adapt the instructions from your 
subcortical ROI-based analysis instructions for cortical gray matter:


mri_vol2vol --mov $PET_DIR/$ID/gtmpvc.output/mgx.gm.nii.gz --reg 
$PET_DIR/$ID/gtmpvc.output/aux/bbpet2anat.lta --tal --talres 2 --o 
$PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz


mri_fwhm --smooth-only --i 
$PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz --fwhm 5 --o 
$PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm05.nii.gz --mask 
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/brainmask.mgz


Can someone confirm or correct these commands? I am especially 
concerned that I have selected the wrong mask.


Thanks you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center



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Re: [Freesurfer] PetSurfer: subcortical volume-based analysis

[Douglas N. Greve]

If you want to do an ROI analysis using FS-based ROIs, you should do 
that at the individual level. Resample the PET to the anatoimical space, 
then run mri_segstats passing the PET with --i and using --seg to spec 
the segmentation. If you really want to do it in MNI305 space, then it 
is the same thing just using the MNI305-based (2mm) segmentation


On 2/14/2022 6:11 PM, Jennifer Bramen wrote:


External Email - Use Caution

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have completed 
all of the steps from the PetSurfer wiki. I now have the preprocessed, 
averaged, resampled, smoothed PET data in MNI305 space which is 
constrained to the subcortical gray matter mask.


*How do I extract mean intensity within all of the subcortical ROI?*

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center

1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865  | *Fax: *310-315-4069


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[Freesurfer] PetSurfer: CORTICAL volume-based analysis

[Jennifer Bramen]

External Email - Use Caution

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I am following the steps 
from the PetSurfer wiki. I see instructions for how to do a cortical 
surface-based group analysis. I also see how to do a subcortical ROI-based 
analysis. However, I cannot find detailed instructions for performing a 
cortical ROI-based analysis.



This is how I think I should adapt the instructions from your subcortical 
ROI-based analysis instructions for cortical gray matter:

mri_vol2vol --mov $PET_DIR/$ID/gtmpvc.output/mgx.gm.nii.gz --reg 
$PET_DIR/$ID/gtmpvc.output/aux/bbpet2anat.lta --tal --talres 2 --o 
$PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz

mri_fwhm --smooth-only --i $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm00.nii.gz 
--fwhm 5 --o $PET_DIR/$ID/gtmpvc.output/gm.mni305.2mm.sm05.nii.gz --mask 
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/brainmask.mgz


Can someone confirm or correct these commands? I am especially concerned that I 
have selected the wrong mask.


Thanks you!
Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center



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[Freesurfer] PetSurfer: subcortical volume-based analysis

[Jennifer Bramen]

External Email - Use Caution

Dear Freesurfer Developers

I am doing an ROI--based amyloid PET scan analysis. I have completed all of the 
steps from the PetSurfer wiki. I now have the preprocessed, averaged, 
resampled, smoothed PET data in MNI305 space which is constrained to the 
subcortical gray matter mask.

How do I extract mean intensity within all of the subcortical ROI?

Thank you!

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069


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Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

[Jennifer Bramen]

External Email - Use Caution

Hi Doug

I think I figured out my answer.  ADNI does 4 volume Amyloid PET analyses by 
averaging the 4 volumes together. I do not need to do kinetic modeling. I hope 
this helps someone else in the same situation in the future.

Thanks!
Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404



From:  on behalf of Jennifer Bramen 

Reply-To: Freesurfer support list 
Date: Monday, February 7, 2022 at 9:50 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value 
[1][1]


External Email - Use Caution
Hi Doug

I think my first question should be “do I need to do KM?”. This is an amyloid 
scan and I want to estimate intensity within regions of interest.  Do I need KM 
to estimate mean intensity?

This is what I know about the timing of the 4 amyloid PET volumes:

5 min (300 sec) – Amyloid Brain

  *   (5 minx 4 beds)
  *   40 min uptake
  *   10 mCi IV injection

Can I just create a mean volume from this image or some other simple metric 
instead of KM?

Thanks for your help.

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Friday, February 4, 2022 at 5:09 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value 
[1][1]

Can you send all the terminal output?  Also, you only have 4 time points in 
time.dat. Is this accurate? It's going to be hard to do KM with 4 time points.
On 1/31/2022 5:00 PM, Jennifer Bramen wrote:

External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to analyze amyloid PET data using  PETSurfer. I am trying to do 
kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one 
using the wiki instructions and the other using the tutorial ROI-based approach)

mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 
$PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 
--no-est-fwhm --nii.gz; done


 mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 
$PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o 
$PET_DIR/PREV_019/mrtm1.roi --nii.gz;done

Both times I get this error:

error: MatrixReadTxT: could not scan value [1][1]

I have opened all of the .dat files using my text editor (nano) and they seem 
ok. I have tried this in other subjects and I get the same error.

I searched the list and I cannot find any discussion regarding this error using 
mri_glmfit and PET data.  Anything you can do to help me troubleshoot this 
error would be greatly appreciated!!! Attached is my time.dat file (I think 
this is the most likely culprit).




Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center









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Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

[Jennifer Bramen]

External Email - Use Caution

Hi Doug

I think my first question should be “do I need to do KM?”. This is an amyloid 
scan and I want to estimate intensity within regions of interest.  Do I need KM 
to estimate mean intensity?

This is what I know about the timing of the 4 amyloid PET volumes:

5 min (300 sec) – Amyloid Brain

  *   (5 minx 4 beds)
  *   40 min uptake
  *   10 mCi IV injection

Can I just create a mean volume from this image or some other simple metric 
instead of KM?

Thanks for your help.

Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
Phone: 310-525-0865  | Fax: 310-315-4069


From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Friday, February 4, 2022 at 5:09 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value 
[1][1]

Can you send all the terminal output?  Also, you only have 4 time points in 
time.dat. Is this accurate? It's going to be hard to do KM with 4 time points.
On 1/31/2022 5:00 PM, Jennifer Bramen wrote:

External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to analyze amyloid PET data using  PETSurfer. I am trying to do 
kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one 
using the wiki instructions and the other using the tutorial ROI-based approach)

mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 
$PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 
--no-est-fwhm --nii.gz; done


 mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 
$PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o 
$PET_DIR/PREV_019/mrtm1.roi --nii.gz;done

Both times I get this error:

error: MatrixReadTxT: could not scan value [1][1]

I have opened all of the .dat files using my text editor (nano) and they seem 
ok. I have tried this in other subjects and I get the same error.

I searched the list and I cannot find any discussion regarding this error using 
mri_glmfit and PET data.  Anything you can do to help me troubleshoot this 
error would be greatly appreciated!!! Attached is my time.dat file (I think 
this is the most likely culprit).




Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center







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Re: [Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

[Douglas N. Greve]

Can you send all the terminal output?  Also, you only have 4 time points 
in time.dat. Is this accurate? It's going to be hard to do KM with 4 
time points.


On 1/31/2022 5:00 PM, Jennifer Bramen wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to analyze amyloid PET data using  PETSurfer. I am 
trying to do kinetic modeling and I am on the MRTM1 step. I have tried 
this two ways (one using the wiki instructions and the other using the 
tutorial ROI-based approach)


mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz 
--mrtm1 $PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat 
$PET_DIR/time.dat --o mrtm1 --no-est-fwhm --nii.gz; done


 mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 
$PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o 
$PET_DIR/PREV_019/mrtm1.roi --nii.gz;done


Both times I get this error:

*error: MatrixReadTxT: could not scan value [1][1]*

I have opened all of the .dat files using my text editor (nano) and 
they seem ok. I have tried this in other subjects and I get the same 
error.


I searched the list and I cannot find any discussion regarding this 
error using mri_glmfit and PET data.  Anything you can do to help me 
troubleshoot this error would be greatly appreciated!!! Attached is my 
time.dat file (I think this is the most likely culprit).


Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & 
Foundation | Providence Saint John's Health Center



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[Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

[Jennifer Bramen]

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to analyze amyloid PET data using  PETSurfer. I am trying to do 
kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one 
using the wiki instructions and the other using the tutorial ROI-based approach)

mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/km.hb.tac.nii.gz --mrtm1 
$PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o mrtm1 
--no-est-fwhm --nii.gz; done


 mri_glmfit --y $PET_DIR/PREV_019/gtmpvc.output/gtm.nii.gz --mrtm1 
$PET_DIR/PREV_019/gtmpvc.output/km.ref.tac.dat $PET_DIR/time.dat --o 
$PET_DIR/PREV_019/mrtm1.roi --nii.gz;done

Both times I get this error:

error: MatrixReadTxT: could not scan value [1][1]

I have opened all of the .dat files using my text editor (nano) and they seem 
ok. I have tried this in other subjects and I get the same error.

I searched the list and I cannot find any discussion regarding this error using 
mri_glmfit and PET data.  Anything you can do to help me troubleshoot this 
error would be greatly appreciated!!! Attached is my time.dat file (I think 
this is the most likely culprit).




Warm regards,


Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute & Foundation | 
Providence Saint John's Health Center





time.dat
Description: time.dat
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[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

[Zhener Zhang]

External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command: 

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off: 
One is to set the point-spread function to 0 by adding “—psf 0”, 
The other one is to get rid of “—psf” altogether and add “—no-tfe”. 

We tried both and they produced slightly different results. The second method 
“—no-tfe” produced lower uptake values for each ROI. Which one would you 
recommend to properly turn PVC off? Thanks in advance! 

Best regards, 
Zhener

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[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

[Zhener Zhang]

External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command: 

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off: 
One is to set the point-spread function to 0 by adding “—psf 0”, 
The other one is to get rid of “—psf” altogether and add “—no-tfe”. 

We tried both and they produced slightly different results. The second method 
“—no-tfe” produced lower uptake values for each ROI. Which one would you 
recommend to properly turn PVC off? Thanks in advance! 

Best regards, 
Zhener

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[Freesurfer] PETSurfer: Which is the right way to turn off PVC?

[Zhener Zhang]

External Email - Use Caution

Hello,

I have a question regarding the following PETSurfer command: 

mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output

I have been trying to run the analysis without applying partial volume 
correction, but it seems like there are two ways to turn it off: 
One is to set the point-spread function to 0 by adding “—psf 0”, 
The other one is to get rid of “—psf” altogether and add “—no-tfe”. 

We tried both and they produced slightly different results. The second method 
“—no-tfe” produced lower uptake values for each ROI. Which one would you 
recommend to properly turn PVC off? Thanks in advance! 

Best regards, 
Zhener

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Re: [Freesurfer] PETsurfer

[Brusaferri, Ludovica]

Great!

Thanks SO much.

Kindly,
Ludovica


On Nov 3, 2021, at 20:43, Adam Martersteck  wrote:



External Email - Use Caution

PETsurfer wasn't released until the v6.0.0 stable build. You can see it in the 
release notes here: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

I'd suggest downloading the newest release which will have the most updated 
code.

You should be able to run PETsurfer from FS builds v6.0, v7.1, v7.2+ (gtmseg, 
mri_gtmpvc, etc.) on v5.3.0 reconstructions. (Note: it's often recommended for 
reproducibility sake to use the same version of FS if you can spare the compute 
time).

On Wed, Nov 3, 2021 at 8:07 AM Brusaferri, Ludovica 
mailto:lbrusafe...@mgh.harvard.edu>> wrote:
Hi!

Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal 
commands such as tkregister it works , but if I try PETsurfer commands I have 
errors such as "mri_gtmpvc: Command not found”.
Any idea?

Thank you,
Ludovica

On Nov 3, 2021, at 10:05, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

There is nothing special you have to do. What version of FS do you have? You 
still have to source the FS environment. If you can run recon-all, you should 
be able to run PETsurfer

On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
Hi!

I have been using freesurfer regularly and I am now trying to implement a few 
commands from PETsurfer MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer.
It seems like I cannot use any of the commands listed in the wiki (such as 
gtmseg or mri_coreg), although they should be part of the freesurfer package 
(as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline 
to install the PETsurfer extension? If so, could you please guide me through?
Thanks so much in advance!

Kindly,
Ludovica



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Re: [Freesurfer] PETsurfer

[Adam Martersteck]

External Email - Use Caution

PETsurfer wasn't released until the v6.0.0 stable build. You can see it in
the release notes here:
https://secure-web.cisco.com/1n9uot8CDL1X4zb4xQXVdkvdqbv2ngmmjy0xI-YpaJo1tCft8AUJ0fOq2tnIi9H-neObzRYbNnzQ_f-6Te5NpdO_gdoIcUF7wBpGrIgl62EZEaig2VymVFjCNARkni1wUTJ13czIyMTklgwK4iZYXxPXCi62hXdypysMt1AovGhIBjCBbxwxARFiBo7UK4yxCu_DkX3qIclp985He7UPMP41zXb2euSPBiCtR_UvI2e1n30GWDH8BltpJ7syxjN2U7Gvsjo_ROof_krSJUUDh2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes

I'd suggest downloading the newest release which will have the most updated
code.

You should be able to run PETsurfer from FS builds v6.0, v7.1, v7.2+
(gtmseg, mri_gtmpvc, etc.) on v5.3.0 reconstructions. (Note: it's often
recommended for reproducibility sake to use the same version of FS if you
can spare the compute time).

On Wed, Nov 3, 2021 at 8:07 AM Brusaferri, Ludovica <
lbrusafe...@mgh.harvard.edu> wrote:

> Hi!
>
> Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal
> commands such as tkregister it works , but if I try PETsurfer commands I
> have errors such as "mri_gtmpvc: Command not found”.
> Any idea?
>
> Thank you,
> Ludovica
>
> On Nov 3, 2021, at 10:05, Douglas N. Greve  wrote:
>
> There is nothing special you have to do. What version of FS do you have?
> You still have to source the FS environment. If you can run recon-all, you
> should be able to run PETsurfer
>
> On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
>
> Hi!
>
> I have been using freesurfer regularly and I am now trying to implement a
> few commands from PETsurfer
> https://secure-web.cisco.com/1BqgJn5GtD8lBmMhFIdkypD8JUZh4G9z6XnAbXLEtWVfk5ajdnK2tMbsx-SPWVIKjr-pvrXHZkfmuy822Z5VxuFrJPxx1uk4mN5QrGBjkWDzSIIb2mqQM8GVyIgapEgf8nTKrJooRayERS_AT_qr18crszq0A-mVtb3-oyYRRpGnUWMHEYJ0c9HDY4jv0xzEi3hUz7v4hsPpfk4MreO51RBUg69F_vA1eLD3NJOnCWDMFQBWsa9ugagsp6DyfQmNDEP2oIcThnq9fsmkqvQt6zw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer.
> It seems like I cannot use any of the commands listed in the wiki (such as
> gtmseg or mri_coreg), although they should be part of the freesurfer
> package (as PETsurfer is part of freesurfer). Do I need to follow a
> specific pipeline to install the PETsurfer extension? If so, could you
> please guide me through?
> Thanks so much in advance!
>
> Kindly,
> Ludovica
>
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Re: [Freesurfer] PETsurfer

[Brusaferri, Ludovica]

Hi!

Thanks a lot. I have freesurfer 5.3.0 installed. If I type on the terminal 
commands such as tkregister it works , but if I try PETsurfer commands I have 
errors such as "mri_gtmpvc: Command not found”.
Any idea?

Thank you,
Ludovica

> On Nov 3, 2021, at 10:05, Douglas N. Greve  wrote:
> 
> There is nothing special you have to do. What version of FS do you have? You 
> still have to source the FS environment. If you can run recon-all, you should 
> be able to run PETsurfer
> 
> On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:
>> Hi!
>> 
>> I have been using freesurfer regularly and I am now trying to implement a 
>> few commands from PETsurfer 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
>> .
>> It seems like I cannot use any of the commands listed in the wiki (such as 
>> gtmseg or mri_coreg), although they should be part of the freesurfer package 
>> (as PETsurfer is part of freesurfer). Do I need to follow a specific 
>> pipeline to install the PETsurfer extension? If so, could you please guide 
>> me through?
>> Thanks so much in advance!
>> 
>> Kindly,
>> Ludovica 
>> 
>> 
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Re: [Freesurfer] PETsurfer

[Douglas N. Greve]

There is nothing special you have to do. What version of FS do you have? 
You still have to source the FS environment. If you can run recon-all, 
you should be able to run PETsurfer


On 11/1/2021 12:26 PM, Brusaferri, Ludovica wrote:

Hi!

I have been using freesurfer regularly and I am now trying to 
implement a few commands from PETsurfer 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer.
It seems like I cannot use any of the commands listed in the wiki 
(such as gtmseg or mri_coreg), although they should be part of the 
freesurfer package (as PETsurfer is part of freesurfer). Do I need to 
follow a specific pipeline to install the PETsurfer extension? If so, 
could you please guide me through?

Thanks so much in advance!

Kindly,
Ludovica

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[Freesurfer] PETsurfer

[Brusaferri, Ludovica]

Hi!

I have been using freesurfer regularly and I am now trying to implement a few 
commands from PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer 
.
It seems like I cannot use any of the commands listed in the wiki (such as 
gtmseg or mri_coreg), although they should be part of the freesurfer package 
(as PETsurfer is part of freesurfer). Do I need to follow a specific pipeline 
to install the PETsurfer extension? If so, could you please guide me through?
Thanks so much in advance!

Kindly,
Ludovica 

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Re: [Freesurfer] PETSurfer voxelwise statistic

[Greve, Douglas N.,Ph.D.]

Traditionally, MG analysis is only run on GM. In principle, it is possible to 
run it on WM, but we don't offer that as an option.

On 11/25/2020 8:16 AM, Boris Rauchmann wrote:

External Email - Use Caution

Dear all,

How can I run a voxelwise statistic using grey and white matter uptake? 
mgx.ctxgm.nii.gz and the other files in output all only include gm as I 
understand.

My goal is to run whole brain volume-based analysis. Like in this example for 
subcortical analysis:

mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta
--tal --talres 2  --o subctxgm.mni305.2mm.sm00.nii.gz

Thanks,
Boris





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Re: [Freesurfer] PETSurfer

[Greve, Douglas N.,Ph.D.]

One way you can do it is to specify all the GM ROIs with --rescale Id1 Id2 ...
Otherwise, you can run fscalc, eg,

fscalc mgx.ctxgm.nii.gz div `cat global.gm.dat ` -mul 100 -o 
mgx.ctxgm.rescaled.nii.gz



On 11/20/2020 11:44 AM, Boris Rauchmann wrote:

External Email - Use Caution

Dear all,

How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean 
intensity using PETSufer? Is there a command to use in mri_gtmpvc like 
--rescale X?
I know that I can find the mean in  global.gm.dat and I can use that value for 
scaling the atlas based results in gtm.stats.dat but how can I easily scale the 
image?

Thanks,
Boris






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[Freesurfer] PETSurfer voxelwise statistic

[Boris Rauchmann]

External Email - Use Caution

Dear all,

How can I run a voxelwise statistic using grey and white matter uptake?
mgx.ctxgm.nii.gz and the other files in output all only include gm as I
understand.

My goal is to run whole brain volume-based analysis. Like in this example
for subcortical analysis:

mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta
--tal --talres 2  --o subctxgm.mni305.2mm.sm00.nii.gz


Thanks,
Boris
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[Freesurfer] PETSurfer

[Boris Rauchmann]

External Email - Use Caution

Dear all,

How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean
intensity using PETSufer? Is there a command to use in mri_gtmpvc like
--rescale X?
I know that I can find the mean in  global.gm.dat and I can use that value
for scaling the atlas based results in gtm.stats.dat but how can I easily
scale the image?

Thanks,
Boris
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[Freesurfer] PETSURFER for AV1451

[Shane Schofield]

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Hi PETSURFERs, 
A quick question to the group: Does any one have experience using PETSURFER on 
dynamic AV1451 scans? How can I know whether the MRTM1 or MRTM2 using midbrains 
(due to off target AV1451 binding) is suitable for my data? 
Thank you!
Best Wishes,Shane
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Re: [Freesurfer] Petsurfer - negative values after RBV partial volume correction

[Douglas Greve]

Yes, this is not unusual. The GTM (which RBV is based on) is just a GLM 
where it uses a linear model to estimate the ROI intensities. There are 
no constraints on positivity. When the model is not exactly correct 
(which it never will be) it is possible to get negative values. Usually 
this only happens in small ROIs and/or low uptake regions. Why might the 
model not be perfect? It could be a number of things:

1. the MRI-PET registration is inaccurate
2. the MRI segmentation is inaccurate
3. the ideal segmentation is not reflected by the MRI segmentation (eg, 
one of the segmentations has a hot spot)


It could also be the case that the OSEM positivity constraint causes 
bias in low uptake regions (the GLM expects two-sided Gaussian noise)



On 8/28/20 7:27 PM, Albrecht, Daniel S. wrote:


Hello,

I’ve been running RBV partial volume correction on some amyloid PET 
data recently using mri_gtmpvc, and for ~90% of subjects the resulting 
rbv.nii.gz looks as expected with the exception of negative values in 
the bilateral accumbens (see attached image, thresholded from 0-4000 
in scanner units). Any ideas why this might be happening?


This is the command I’ve been using:

mri_gtmpvc --i $PETimg \
--reg $identity_mtrx  \
--seg $FSdir/${subject}/mri/gtmseg.mgz \
--psf 6 --default-seg-merge --auto-mask PSF .01 --rbv \
--no-rescale --threads 8 \
--o $outname

Thanks very much,

Dan


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Re: [Freesurfer] PETSurfer questions part III

[Douglas N. Greve]

On 7/24/2020 10:27 AM, Ferraro, Pilar wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> All the analyses have been run with FS version 6 indeed.
> If you confirm the commands below are correct, I therefore assume I should 
> rerun all the analyses using FS 7.1.
>
> I just have few remaining questions:
>
> 1. Are there any other ROIs more than the pons that you have changed from WM 
> to GM in FS 7.1?
Ventral Diencephalon (VentralDC) is now GM.
>
> 2. Is the same problem of WM/GM classification affecting MZ corrected uptake 
> estimation? I suppose WM/GM classification should affect only MG since it’s a 
> 3 compartment model, but I’m not sure.
It should not
>
> Many thanks,
>
> Pilar
>
>
>
> Commands:
> 1) With Muller-Gartner (MG):
> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
> Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
>
> Then:
> mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
> gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab — sum 
> MG_ROI.txt
>
> 2) With Meltzer (MZ):
>
> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
> Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 —o gtm_MZ.output
>
> Then:
> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum 
> MZ_ROI.txt
>
>> On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:
>>> External Email - Use Caution
>>>
>>> Many thanks for the reply,
>>>
>>> Yep, unfortunately MG values are always much higher than SGTM ones (in
>>> all the ROIs).
>>> I wonder whether this might be related (for MG and MZ) to the absence
>>> of a normalization using the pons as a reference.
>>>
>>> Indeed, when I look at the file with mean values extracted for each
>>> modality, I see that the pons has always 1000 as mean uptake value for
>>> no PVC and SGTM, while for MG and MZ values in the pons range from
>>> -0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
>> Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you
>> using? In version 6, pons was considered white matter, but I changed it
>> to gray matter in version 7. The bottom line on this is that you cannot
>> compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then
>> its value is bogus.
>>> Below are the commands I?ve used to obtain the MG and MZ values:
>>>
>>> 1) With Muller-Gartner (MG):
>>>
>>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6
>>> --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
>>>
>>> ?Then:
>>>
>>> mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg
>>> gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum
>>> MG_ROI.txt
>>>
>>> 2) With Meltzer (MZ):
>>>
>>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6
>>> --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o
>>> gtm_MZ.output
>>>
>>> Then:
>>>
>>> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg
>>> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum
>>> MZ_ROI.txt
>>>
>>>
>>> Do you recognize any errors in the commands?
>>>
>>>
>>> Many thanks,
>>>
>>> Pilar
>>>
>>>
>>>
>>>
>>>
>>>> Message: 13
>>>> Date: Thu, 16 Jul 2020 10:19:32 -0400
>>>> From: "Douglas N. Greve" >>> <mailto:dgr...@mgh.harvard.edu>>
>>>> Subject: Re: [Freesurfer] PETSurfer analysis question
>>>> To: >>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>>> Message-ID: >>> <mailto:d56acc7d-3273-4f40-ed17-570a893b2...@mgh.harvard.edu>>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>>
>>>> The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
>>>> I don't put stock in MZ. Is the MG value much higher than SGTM in other
>>>> ROIs? What is your mri_gtmpvc command?
>>>>
>>>>
>>>> On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:
>>>>> External Email - Use Caution
>>>>>
>>>>> Hi Freesurfer experts,
>>>>>
>>>>> I?ve run a PETSurfer analysis in order to compare mean?uptake values
>>>>

[Freesurfer] PETSurfer questions part III

[Ferraro, Pilar]

External Email - Use Caution

Hi Douglas,

All the analyses have been run with FS version 6 indeed. 
If you confirm the commands below are correct, I therefore assume I should 
rerun all the analyses using FS 7.1.

I just have few remaining questions:

1. Are there any other ROIs more than the pons that you have changed from WM to 
GM in FS 7.1?

2. Is the same problem of WM/GM classification affecting MZ corrected uptake 
estimation? I suppose WM/GM classification should affect only MG since it’s a 3 
compartment model, but I’m not sure.

Many thanks,

Pilar



Commands:
1) With Muller-Gartner (MG):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output

Then:
mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab — sum MG_ROI.txt

2) With Meltzer (MZ):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 —o gtm_MZ.output

Then:
mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt

> 
> On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:
>> 
>> External Email - Use Caution
>> 
>> Many thanks for the reply,
>> 
>> Yep, unfortunately MG values are always much higher than SGTM ones (in 
>> all the ROIs).
>> I wonder whether this might be related (for MG and MZ) to the absence 
>> of a normalization using the pons as a reference.
>> 
>> Indeed, when I look at the file with mean values extracted for each 
>> modality, I see that the pons has always 1000 as mean uptake value for 
>> no PVC and SGTM, while for MG and MZ values in the pons range from 
>> -0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
> Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you 
> using? In version 6, pons was considered white matter, but I changed it 
> to gray matter in version 7. The bottom line on this is that you cannot 
> compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then 
> its value is bogus.
>> 
>> Below are the commands I?ve used to obtain the MG and MZ values:
>> 
>> 1) With Muller-Gartner (MG):
>> 
>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
>> --seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
>> 
>> ?Then:
>> 
>> mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
>> gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum 
>> MG_ROI.txt
>> 
>> 2) With Meltzer (MZ):
>> 
>> mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
>> --seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o 
>> gtm_MZ.output
>> 
>> Then:
>> 
>> mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
>> gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum 
>> MZ_ROI.txt
>> 
>> 
>> Do you recognize any errors in the commands?
>> 
>> 
>> Many thanks,
>> 
>> Pilar
>> 
>> 
>> 
>> 
>> 
>>> 
>>> Message: 13
>>> Date: Thu, 16 Jul 2020 10:19:32 -0400
>>> From: "Douglas N. Greve" >> <mailto:dgr...@mgh.harvard.edu>>
>>> Subject: Re: [Freesurfer] PETSurfer analysis question
>>> To: >> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>> Message-ID: >> <mailto:d56acc7d-3273-4f40-ed17-570a893b2...@mgh.harvard.edu>>
>>> Content-Type: text/plain; charset="utf-8"
>>> 
>>> 
>>> The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
>>> I don't put stock in MZ. Is the MG value much higher than SGTM in other
>>> ROIs? What is your mri_gtmpvc command?
>>> 
>>> 
>>> On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:
>>>> 
>>>> External Email - Use Caution
>>>> 
>>>> Hi Freesurfer experts,
>>>> 
>>>> I?ve run a PETSurfer analysis in order to compare mean?uptake values
>>>> of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
>>>> However, I?ve now extracted the mean values and they are extremely
>>>> heterogeneous.
>>>> As an example, the same ROI (lh banks of the superior temporal sulcus)
>>>> has the following uptake values:
>>>> 
>>>> No PVC= 1.709
>>>> SGTM= 2.495
>>>> MG= 23.847
>>>> MZ= 15.564
>>>> 
>>>> I?m particularly 

Re: [Freesurfer] PETSurfer questions - Part II

[Douglas N. Greve]

On 7/20/2020 2:56 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Many thanks for the reply,

Yep, unfortunately MG values are always much higher than SGTM ones (in 
all the ROIs).
I wonder whether this might be related (for MG and MZ) to the absence 
of a normalization using the pons as a reference.


Indeed, when I look at the file with mean values extracted for each 
modality, I see that the pons has always 1000 as mean uptake value for 
no PVC and SGTM, while for MG and MZ values in the pons range from 
-0.02 to -0.65 (for MG) and from 0.94 to 0.99 (for MZ).
Pons should be 1.000 in the SGM and NoPVC. Which version of FS are you 
using? In version 6, pons was considered white matter, but I changed it 
to gray matter in version 7. The bottom line on this is that you cannot 
compute uptake in WM in MG. So, if pons (or any other ROI) is WM, then 
its value is bogus.


Below are the commands I’ve used to obtain the MG and MZ values:

1) With Muller-Gartner (MG):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
--seg Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output


 Then:

mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum 
MG_ROI.txt


2) With Meltzer (MZ):

mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 
--seg Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o 
gtm_MZ.output


Then:

mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum 
MZ_ROI.txt



Do you recognize any errors in the commands?


Many thanks,

Pilar







Message: 13
Date: Thu, 16 Jul 2020 10:19:32 -0400
From: "Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu>>

Subject: Re: [Freesurfer] PETSurfer analysis question
To: <mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <mailto:d56acc7d-3273-4f40-ed17-570a893b2...@mgh.harvard.edu>>

Content-Type: text/plain; charset="utf-8"


The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
I don't put stock in MZ. Is the MG value much higher than SGTM in other
ROIs? What is your mri_gtmpvc command?


On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Hi Freesurfer experts,

I?ve run a PETSurfer analysis in order to compare mean?uptake values
of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
However, I?ve now extracted the mean values and they are extremely
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus)
has the following uptake values:

No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I?m particularly worried for the huge difference between noPVC - SGTM
values and MG-MZ values.

Any advice? I wonder whether this finding is normal or there is
something I?ve missed.

Many thanks,

Pilar









Il giorno 15 lug 2020, alle ore 6:00 PM,
freesurfer-requ...@nmr.mgh.harvard.edu 
<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>

<mailto:freesurfer-requ...@nmr.mgh.harvard.edu> ha scritto:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>


To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
?for some subjects (Douglas N. Greve)
??2. Re: mri_fieldsign error (Douglas N. Greve)
??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)


--

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:


External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
?-o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"

Re: [Freesurfer] PetSurfer Crashing

[Douglas Greve]

Did you really mean to pass subject/mri/gtmseg.lta ? The registration is 
supposed to be the registration of the input (PET.template.nii.gz) to 
the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz 
to the anatomical.


On 7/20/20 11:21 AM, Crawford, Anna wrote:


External Email - Use Caution

Hello,


I am trying to run the PetSurfer process for the first time. I was 
able to run gtmseg and mri_coreg which seemed to go okay. When I tried 
running mri_gtmpvc, it is crashing, but I am not sure why. The command 
I am using and output are below. Do you have any guidance as to what 
is going wrong?



Thank you,

Anna



mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg 
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz  
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o 
subject/gtmpvc.output

Loading input ../CTPET/PET.template.nii.gz
  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/
cd /mnt/autofs/netRAID18/7T/study709/S2sdt
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg 
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz 
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o 
subject/gtmpvc.output

sysname  Linux
hostname fmri15
machine  x86_64
user crawforda
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
20 avail.processors, using 1
Creating output directory subject/gtmpvc.output
Loading seg for gtm subject/mri/gtmseg.mgz
Loading seg ctab subject/mri/gtmseg.ctab
Reading subject/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
done with seg vol
maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Automask, reducing FOV
region 256 256 109 reduced to 21 11 3  235 245 106
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.97615814209e-01 0.000e+00 -8.381903171539307e-09 
-7.62939453125e-06
7.450580596923828e-09 9.98807907104e-01 0.000e+00 
0.000e+00
-7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 
-1.52587890625e-05
0.000e+00 0.000e+00 0.000e+00 
9.99403953552e-01

src volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 
-2.000e+01

dst volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 
-2.000e+01

subject subject
fscale 0.15
LTA 1 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.99403953552e-01 0.000e+00 0.000e+00 
-2.09237060547e+01
0.000e+00 9.99403953552e-01 0.000e+00 
-1.10762939453e+01
0.000e+00 0.000e+00 1.000e+00 
-3.000e+00
0.000e+00 0.000e+00 0.000e+00 
1.000e+00

src volume info
valid = 1  # volume info valid
filename = ../CTPET/PET.template.nii.gz
volume = 256 256 109
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 
2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 
0.000e+00
yras   = -0.000e+00 1.000e+00 
0.000e+00
zras   = -0.000e+00 -0.000e+00 
1.000e+00

cras   = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03
dst volume info
valid = 1  # volume info valid
filename =
volume = 235 245 106
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 
2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 
0.000e+00
yras   = -0.000e+00 1.000e+00 
0.000e+00
zras   = -0.000e+00 -0.000e+00 
1.000e+00
cras   = -1.861288452148438e+01 1.840597229003906e+02 
1.250690063476562e+03

--
Data load time 10.9 sec
nmask = 3714389, nsegs = 100, excluding 

[Freesurfer] PetSurfer Crashing

[Crawford, Anna]

External Email - Use Caution

Hello,


I am trying to run the PetSurfer process for the first time. I was able to run 
gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, 
it is crashing, but I am not sure why. The command I am using and output are 
below. Do you have any guidance as to what is going wrong?


Thank you,

Anna



mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 
6 --seg subject/mri/gtmseg.mgz  --default-seg-merge --auto-mask PSF .01 --mgx 
.01 --o subject/gtmpvc.output
Loading input ../CTPET/PET.template.nii.gz
  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/
cd /mnt/autofs/netRAID18/7T/study709/S2sdt
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 
6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 
.01 --o subject/gtmpvc.output
sysname  Linux
hostname fmri15
machine  x86_64
user crawforda
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
20 avail.processors, using 1
Creating output directory subject/gtmpvc.output
Loading seg for gtm subject/mri/gtmseg.mgz
Loading seg ctab subject/mri/gtmseg.ctab
Reading subject/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
done with seg vol
maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Automask, reducing FOV
region 256 256 109 reduced to 21 11 3  235 245 106
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.97615814209e-01 0.000e+00 -8.381903171539307e-09 
-7.62939453125e-06
7.450580596923828e-09 9.98807907104e-01 0.000e+00 
0.000e+00
-7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 
-1.52587890625e-05
0.000e+00 0.000e+00 0.000e+00 
9.99403953552e-01
src volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 -2.000e+01
dst volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 -2.000e+01
subject subject
fscale 0.15
LTA 1 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.99403953552e-01 0.000e+00 0.000e+00 
-2.09237060547e+01
0.000e+00 9.99403953552e-01 0.000e+00 
-1.10762939453e+01
0.000e+00 0.000e+00 1.000e+00 
-3.000e+00
0.000e+00 0.000e+00 0.000e+00 
1.000e+00
src volume info
valid = 1  # volume info valid
filename = ../CTPET/PET.template.nii.gz
volume = 256 256 109
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 0.000e+00
yras   = -0.000e+00 1.000e+00 0.000e+00
zras   = -0.000e+00 -0.000e+00 1.000e+00
cras   = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03
dst volume info
valid = 1  # volume info valid
filename =
volume = 235 245 106
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 0.000e+00
yras   = -0.000e+00 1.000e+00 0.000e+00
zras   = -0.000e+00 -0.000e+00 1.000e+00
cras   = -1.861288452148438e+01 1.840597229003906e+02 1.250690063476562e+03
--
Data load time 10.9 sec
nmask = 3714389, nsegs = 100, excluding segid=0
FWHM: 6 6 6
Std:  2.54797 2.54797 2.54797
nPad 10, PadThresh 0.0001
Checking Ref Ids
Segmentations used for rescaling
 174 Pons
Computing Seg PVF
Segmentation fault (core dumped)


Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in 

[Freesurfer] PETSurfer questions - Part II

[Ferraro, Pilar]

External Email - Use Caution

Many thanks for the reply,

Yep, unfortunately MG values are always much higher than SGTM ones (in all the 
ROIs).
I wonder whether this might be related (for MG and MZ) to the absence of a 
normalization using the pons as a reference.

Indeed, when I look at the file with mean values extracted for each modality, I 
see that the pons has always 1000 as mean uptake value for no PVC and SGTM, 
while for MG and MZ values in the pons range from -0.02 to -0.65 (for MG) and 
from 0.94 to 0.99 (for MZ).

Below are the commands I’ve used to obtain the MG and MZ values:
1) With Muller-Gartner (MG):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --mgx .01 --o gtm_MG.output
 Then:
mri_segstats --i gtm_MG.output/mgx.ctxgm.nii.gz --seg 
gtm_MG.output/aux/seg.nii.gz --ctab gtm_MG.output/aux/seg.ctab --sum MG_ROI.txt
2) With Meltzer (MZ):
mri_gtmpvc --i ../Subj_PET_image --reg Subj_template.reg.lta --psf 6 --seg 
Subj_gtmseg.mgz --default-seg-merge --Meltzer .1 .1 1 --o gtm_MZ.output
Then:
mri_segstats --i gtm_MZ.output/meltzer.nii.gz --seg 
gtm_MZ.output/aux/seg.nii.gz --ctab gtm_MZ.output/aux/seg.ctab --sum MZ_ROI.txt

Do you recognize any errors in the commands?

Many thanks,

Pilar






Message: 13
Date: Thu, 16 Jul 2020 10:19:32 -0400
From: "Douglas N. Greve" mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] PETSurfer analysis question
To: mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
mailto:d56acc7d-3273-4f40-ed17-570a893b2...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"


The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
I don't put stock in MZ. Is the MG value much higher than SGTM in other
ROIs? What is your mri_gtmpvc command?


On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:

External Email - Use Caution

Hi Freesurfer experts,

I?ve run a PETSurfer analysis in order to compare mean?uptake values
of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
However, I?ve now extracted the mean values and they are extremely
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus)
has the following uptake values:

No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I?m particularly worried for the huge difference between noPVC - SGTM
values and MG-MZ values.

Any advice? I wonder whether this finding is normal or there is
something I?ve missed.

Many thanks,

Pilar








Il giorno 15 lug 2020, alle ore 6:00 PM,
freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>
<mailto:freesurfer-requ...@nmr.mgh.harvard.edu> ha scritto:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
?for some subjects (Douglas N. Greve)
??2. Re: mri_fieldsign error (Douglas N. Greve)
??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)


--

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:

External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
?-o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"###
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###"

It simply stopped running there.

Others did finish running, but instead got a se

Re: [Freesurfer] PETSurfer analysis question

[Douglas N. Greve]

The NoPVC and SGTM values are reasonable. The MG value is pretty crazy. 
I don't put stock in MZ. Is the MG value much higher than SGTM in other 
ROIs? What is your mri_gtmpvc command?



On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Hi Freesurfer experts,

I’ve run a PETSurfer analysis in order to compare mean uptake values 
of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
However, I’ve now extracted the mean values and they are extremely 
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus) 
has the following uptake values:


No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I’m particularly worried for the huge difference between noPVC - SGTM 
values and MG-MZ values.


Any advice? I wonder whether this finding is normal or there is 
something I’ve missed.


Many thanks,

Pilar








Il giorno 15 lug 2020, alle ore 6:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu 
 ha scritto:


Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu 

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
 for some subjects (Douglas N. Greve)
  2. Re: mri_fieldsign error (Douglas N. Greve)
  3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)


--

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:


External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
 -o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"###
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###"

It simply stopped running there.

Others did finish running, but instead got a segmentation fault error.

What could I do? I have Mac High Sierra.


Annelies

Annelies van't Westeinde?| PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskav?gen 37A
+46 760967499
annelies.vant.westei...@ki.se | ki.se 
__
Karolinska Institutet ? a medical university



/N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta
att KI kommer att behandla dina personuppgifter. /H?r finns
information om hur KI behandlar personuppgifter
.


/Sending email to Karolinska Institutet (KI) will result in KI
processing your personal data./ You can read more about KI?s
processing of personal data here
.


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--

Message: 2
Date: Wed, 15 Jul 2020 11:14:53 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] mri_fieldsign error
To: 
Message-ID: <5364c956-1d58-e69d-5635-6fde5dd41...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I don't know what is going wrong here. One simple thing to check is to
make sure that all the input files have the same number of vertices as
the surface. If that is the case, then upload the subject and input
files using the instructions below

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz 

[Freesurfer] PETSurfer analysis question

[Ferraro, Pilar]

External Email - Use Caution

Hi Freesurfer experts,

I’ve run a PETSurfer analysis in order to compare mean uptake values of ROIs 
obtained with different methods: No PVC, SGTM, MG and MZ.
However, I’ve now extracted the mean values and they are extremely 
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus) has the 
following uptake values:

No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I’m particularly worried for the huge difference between noPVC - SGTM values 
and MG-MZ values.

Any advice? I wonder whether this finding is normal or there is something I’ve 
missed.

Many thanks,

Pilar








Il giorno 15 lug 2020, alle ore 6:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu
 ha scritto:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
 for some subjects (Douglas N. Greve)
  2. Re: mri_fieldsign error (Douglas N. Greve)
  3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)


--

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: 
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:

External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
 -o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"###
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
###"

It simply stopped running there.

Others did finish running, but instead got a segmentation fault error.

What could I do? I have Mac High Sierra.


Annelies

Annelies van't Westeinde?| PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskav?gen 37A
+46 760967499
annelies.vant.westei...@ki.se | ki.se 
__
Karolinska Institutet ? a medical university



/N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta
att KI kommer att behandla dina personuppgifter. /H?r finns
information om hur KI behandlar personuppgifter
.


/Sending email to Karolinska Institutet (KI) will result in KI
processing your personal data./ You can read more about KI?s
processing of personal data here
.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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--

Message: 2
Date: Wed, 15 Jul 2020 11:14:53 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] mri_fieldsign error
To: 
Message-ID: <5364c956-1d58-e69d-5635-6fde5dd41...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I don't know what is going wrong here. One simple thing to check is to
make sure that all the input files have the same number of vertices as
the surface. If that is the case, then upload the subject and input
files using the instructions below

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log? into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary

Re: [Freesurfer] PETsurfer: --usf in gtmseg

[Douglas N. Greve]

yes, that controls how finely the surface-based segmentations are 
resampled into the volume. The surface is semi-continuous so you can 
sample them into the volume as finely as you like. 0.5mm seems to work fine.


On 5/26/2020 4:33 PM, Julie Ottoy wrote:


External Email - Use Caution

Hi,

In PETsurfer gtmseg, there is the --usf (upsampling factor) which is 
by default 2, corresponding to 0.5 mm voxelsize. I was wondering if 
the usf is recommended to be chosen depending on your mri 
voxelsize (eg, usf 1 for 1mm voxelsize of the mri), or will it just 
depend on how "accurate" you want your segmentation to be? Can you 
safely use --usf 2 for an mri with 1mm voxelsize?


Thank you!
best regards
Julie

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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] PETsurfer: --usf in gtmseg

[Julie Ottoy]

External Email - Use Caution

Hi,

In PETsurfer gtmseg, there is the --usf (upsampling factor) which is by
default 2, corresponding to 0.5 mm voxelsize. I was wondering if the usf is
recommended to be chosen depending on your mri voxelsize (eg, usf 1 for 1mm
voxelsize of the mri), or will it just depend on how "accurate" you want
your segmentation to be? Can you safely use --usf 2 for an mri with 1mm
voxelsize?

Thank you!
best regards
Julie
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Re: [Freesurfer] PETSurfer / Questions

[Douglas N. Greve]

On 4/14/2020 5:40 AM, Ferraro, Pilar wrote:


External Email - Use Caution

Dear Freesurfer experts,

We are conducting a PETSurfer analysis, and have some questions on the 
best way to proceed.  Briefly, this is what we have done:


After running the standard Freesurfer analysis an all the T1 images, 
we have generated the segmentation for the GTM.
Afterwards, we have registered the PET images with the anatomicals, 
obtaining the template.reg.lta.
To check the preliminary results without any PVC, we have used the 
template.reg.lta to sample the PET volume onto the surface, with the 
following command:

 mri_vol2surf --mov subject_PET.nii \
 --reg subject_template.reg.lta \
 --projfrac 0.5 --interp nearest \
 --hemi lh --o lh.sig.mgh

We therefore obtained the lh.sig.mgh

First question. Is this procedure correct?
Yes (though you should always check the reg.lta with tkregisterfv). 
Also, why are you calling the output lh.sig.mgh? My question is about 
"sig"; it is not wrong to call it this, but "sig" is usually reserved 
for significance files and I wanted to make sure you were not confused 
by it.

Second question. Is the format of the of the output (.mgh) correct?

Any format (mgh, mgz, nifti) is ok.


In the wiki it is reported that: “If you are not using PVC, you can 
use the template.reg.lta to sample the PET volume onto the surface 
using mri_vol2surf, then apply standard surface-based analysis”.


Third question. At this point should we directly run the mri_glmfit 
with the previously obtained lh.sig.mgh?
This is probably not right. You  will need to run the mri_vol2surf 
command above for each subject to generate an output (and using 
--trgsubject fsaverage to put them into the same space), then 
concatenate all into one file (mri_concat lh.subj1.mgh lh.subj2.mgh ... 
--o lh.all.mgh), then possibly smooth (mris_fwhm), then feed that output 
as input to mri_glmfit.

Like in this way:

 mri_glmfit \
 --y lh.sig.mgh \
 --fsgd fsgd file dods\
 --C cor.mtx file \
--surf fsaverage lh \
--cortex \
--glmdir glmdir

Many thanks for any information you’ll be able to provide,

 Best,

Pilar Maria Ferraro


Il giorno 7 apr 2020, alle ore 6:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu 
 ha scritto:


Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu 

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. vertex number to MNI coordinates (Marina Fern?ndez)
  2. Install Freesurfer on Ubuntu (Stephan)
  3. Re: vertex number to MNI coordinates (Douglas N. Greve)
  4. Re: Install Freesurfer on Ubuntu (Peer Herholz)
  5. Re: Install Freesurfer on Ubuntu (fsbuild)
  6. Permutation with Non-Orthogonal Matrices (Hua, Jessica)
  7. Re: Permutation with Non-Orthogonal Matrices (Douglas N. Greve)
  8. Error in Tracula-all -prep (Salah Showiheen)
  9. hippocampus subfield segmentation using Siemen and GEscans
 (Kate Marvel)
 10. Chorid-plexus in Freesurfer reconall (Lijun An)
 11. Re: Chorid-plexus in Freesurfer reconall (Bruce Fischl)
 12. whether freesurfer version 7 still support GPU (Frank Robert)
 13. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Iglesias Gonzalez, Juan E.)
 14. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)
 15. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Kate Marvel)
 16. Re: whether freesurfer version 7 still support GPU (Frank Robert)
 17. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)


--

Message: 1
Date: Mon, 6 Apr 2020 22:06:24 +0200
From: Marina Fern?ndez 
Subject: [Freesurfer] vertex number to MNI coordinates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Dear Freesurfer experts,

I hope you can help me with the following questions:

1. What is the best way to know the MNI coordinates to which a vertex 
of a

surface corresponds?

2. I have projected the surfaces of the subjects onto the average subject
from this dataset.
Can I know the MNI coordinates corresponding to a vertex of the average
subject of my dataset?
Or do I need to project it onto the fsaverage to know the 
correspondence to

de MNI space?

3. I know that the average surface is constructed by computing the MNI305
coordinate at each vertex,
But how can I obtain the MNI152 coordinates (instead of MNI305) to 
which a

vertex corresponds? (if it is possible).


Thank you very 

Re: [Freesurfer] PETSurfer / Questions

[Ferraro, Pilar]

External Email - Use Caution

Dear Freesurfer experts,

We are conducting a PETSurfer analysis, and have some questions on the best way 
to proceed.  Briefly, this is what we have done:

After running the standard Freesurfer analysis an all the T1 images, we have 
generated the segmentation for the GTM.
Afterwards, we have registered the PET images with the anatomicals, obtaining 
the template.reg.lta.
To check the preliminary results without any PVC, we have used the 
template.reg.lta to sample the PET volume onto the surface, with the following 
command:
 mri_vol2surf --mov subject_PET.nii \
 --reg subject_template.reg.lta \
 --projfrac 0.5 --interp nearest \
 --hemi lh --o lh.sig.mgh

We therefore obtained the lh.sig.mgh

First question. Is this procedure correct?
Second question. Is the format of the of the output (.mgh) correct?

In the wiki it is reported that: “If you are not using PVC, you can use the 
template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, 
then apply standard surface-based analysis”.

Third question. At this point should we directly run the mri_glmfit with the 
previously obtained lh.sig.mgh?
Like in this way:

 mri_glmfit \
 --y lh.sig.mgh \
 --fsgd fsgd file dods\
 --C cor.mtx file \
--surf fsaverage lh \
--cortex \
--glmdir glmdir

Many thanks for any information you’ll be able to provide,

 Best,

Pilar Maria Ferraro


Il giorno 7 apr 2020, alle ore 6:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu
 ha scritto:

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

  1. vertex number to MNI coordinates (Marina Fern?ndez)
  2. Install Freesurfer on Ubuntu (Stephan)
  3. Re: vertex number to MNI coordinates (Douglas N. Greve)
  4. Re: Install Freesurfer on Ubuntu (Peer Herholz)
  5. Re: Install Freesurfer on Ubuntu (fsbuild)
  6. Permutation with Non-Orthogonal Matrices (Hua, Jessica)
  7. Re: Permutation with Non-Orthogonal Matrices (Douglas N. Greve)
  8. Error in Tracula-all -prep (Salah Showiheen)
  9. hippocampus subfield segmentation using Siemen and GE scans
 (Kate Marvel)
 10. Chorid-plexus in Freesurfer reconall (Lijun An)
 11. Re: Chorid-plexus in Freesurfer reconall (Bruce Fischl)
 12. whether freesurfer version 7 still support GPU (Frank Robert)
 13. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Iglesias Gonzalez, Juan E.)
 14. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)
 15. Re: hippocampus subfield segmentation using Siemen and GE
 scans (Kate Marvel)
 16. Re: whether freesurfer version 7 still support GPU (Frank Robert)
 17. Re: whether freesurfer version 7 still support GPU
 (Hoopes, Andrew)


--

Message: 1
Date: Mon, 6 Apr 2020 22:06:24 +0200
From: Marina Fern?ndez 
Subject: [Freesurfer] vertex number to MNI coordinates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Dear Freesurfer experts,

I hope you can help me with the following questions:

1. What is the best way to know the MNI coordinates to which a vertex of a
surface corresponds?

2. I have projected the surfaces of the subjects onto the average subject
from this dataset.
Can I know the MNI coordinates corresponding to a vertex of the average
subject of my dataset?
Or do I need to project it onto the fsaverage to know the correspondence to
de MNI space?

3. I know that the average surface is constructed by computing the MNI305
coordinate at each vertex,
But how can I obtain the MNI152 coordinates (instead of MNI305) to which a
vertex corresponds? (if it is possible).


Thank you very much in advance.

Best regards,
Marina
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Message: 2
Date: Mon, 6 Apr 2020 22:50:15 +0200
From: Stephan 
Subject: [Freesurfer] Install Freesurfer on Ubuntu
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Hi,

ist there an official guideline how to install Freesurfer on Ubuntu?

Best,
Stephan
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Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

[Eckbo, Ryan]

Hi Doug,

Here was my original question (we haven't communicated outside of this thread):

I've recently run into a case the gtmstats uptake (reference region: 
cerebellum) for the  pericarlcarine ROI's are as low as 0.40, however computing 
the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and 
aux/seg.nii.gz, the values are closer to 1, as expected.  This is using 
Freesurfer 6.0, and the PET to anatomical registration looks fine.  Any ideas 
why we get such bad values from the GTM method?

Then you asked, "What is the value for cerebellum in those three scenarious 
(gtm, no pvc, and mgx)?"

So I added the uptake values for the cerebellum to the original table, which 
I've pasted below.  Let me know if there's anything else you need.

Thanks!
Ryan


 vol   |   psf | roi |   gtmstats_uptake |  
 region_mean
---+---+-+---+---
 input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 |  
1.226
 input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 |  
1.0834
 input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex  | 0.981 |  
0.994237
 input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 |  
1.03552
 mgx.ctxgm.nii.gz  | 0 | ctx-rh-pericalcarine| 0.807 |  
1.00685
 mgx.ctxgm.nii.gz  | 0 | ctx-lh-pericalcarine| 0.758 |  
0.887616
 input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 |  
1.19702
 input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine| 0.47  |  
1.05779
 input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex  | 0.984 |  
0.970736
 input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 |  
1.01104
 mgx.ctxgm.nii.gz  | 6 | ctx-rh-pericalcarine| 0.409 |  
0.915328
 mgx.ctxgm.nii.gz  | 6 | ctx-lh-pericalcarine| 0.47  |  
0.809017






From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, April 1, 2020 10:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

Can you include previous emails so that I have some context as to what you are 
asking?

On 4/1/2020 9:18 AM, Eckbo, Ryan wrote:
Here's a table with the cerebellum uptake values included -- let me know if you 
need more information.

​ vol   |   psf | roi |   gtmstats_uptake | 
  region_mean
---+---+-+---+---
 input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 |  
1.226
 input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 |  
1.0834
 input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex  | 0.981 |  
0.994237
 input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 |  
1.03552
 mgx.ctxgm.nii.gz  | 0 | ctx-rh-pericalcarine| 0.807 |  
1.00685
 mgx.ctxgm.nii.gz  | 0 | ctx-lh-pericalcarine| 0.758 |  
0.887616
 input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 |  
1.19702
 input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine| 0.47  |  
1.05779
 input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex  | 0.984 |  
0.970736
 input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 |  
1.01104
 mgx.ctxgm.nii.gz  | 6 | ctx-rh-pericalcarine| 0.409 |  
0.915328
 mgx.ctxgm.nii.gz  | 6 | ctx-lh-pericalcarine| 0.47  |  
0.809017

Thanks!
Ryan


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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: Wednesday, March 11, 2020 10:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

What is the value for cerebellum in those three scenarious (gtm, no pvc, and 
mgx)?

On 3/10/2020 12:37 PM, Eckbo, Ryan wrote:
Hello experts,

I've recently run into a case the gtmstats uptake (reference region: 
cerebellum) for the pericarlcarine ROI's are as low as 0.40,
however computing the voxel wise mean using input.rescaled.nii.gz and 
mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1,
as expected:

| vol   | psf | roi

Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

[Douglas N. Greve]

Can you include previous emails so that I have some context as to what 
you are asking?


On 4/1/2020 9:18 AM, Eckbo, Ryan wrote:
Here's a table with the cerebellum uptake values included -- let me 
know if you need more information.


​ vol                   |   psf | roi                     | 
gtmstats_uptake |   region_mean

---+---+-+---+---
 input.rescaled.nii.gz |     0 | ctx-rh-pericalcarine  |             
0.807 |      1.226
 input.rescaled.nii.gz |     0 | ctx-lh-pericalcarine  |             
0.758 |      1.0834
 input.rescaled.nii.gz |     0 | Left-Cerebellum-Cortex  |             
0.981 |      0.994237
 input.rescaled.nii.gz |     0 | Right-Cerebellum-Cortex |             
1.019 |      1.03552
 mgx.ctxgm.nii.gz      |     0 | ctx-rh-pericalcarine  |             
0.807 |      1.00685
 mgx.ctxgm.nii.gz      |     0 | ctx-lh-pericalcarine  |             
0.758 |      0.887616
 input.rescaled.nii.gz |     6 | ctx-rh-pericalcarine  |             
0.409 |      1.19702
 input.rescaled.nii.gz |     6 | ctx-lh-pericalcarine  |             
0.47  |      1.05779
 input.rescaled.nii.gz |     6 | Left-Cerebellum-Cortex  |             
0.984 |      0.970736
 input.rescaled.nii.gz |     6 | Right-Cerebellum-Cortex |             
1.016 |      1.01104
 mgx.ctxgm.nii.gz      |     6 | ctx-rh-pericalcarine  |             
0.409 |      0.915328
 mgx.ctxgm.nii.gz      |     6 | ctx-lh-pericalcarine  |             
0.47  |      0.809017


Thanks!
Ryan


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, March 11, 2020 10:01 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean 
is fine
What is the value for cerebellum in those three scenarious (gtm, no 
pvc, and mgx)?


On 3/10/2020 12:37 PM, Eckbo, Ryan wrote:

Hello experts,

I've recently run into a case the gtmstats uptake (reference region: 
cerebellum) for the pericarlcarine ROI's are as low as 0.40,
however computing the voxel wise mean using input.rescaled.nii.gz and 
mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1,

as expected:

| vol                 | psf | roi                  | gtmstats_uptake 
| mean_uptake |
| - | --- |  | 
--- | --- |
| input.rescaled.nii.gz |   0 | ctx-rh-pericalcarine |       0.807 | 
     1.226… |
| input.rescaled.nii.gz |   0 | ctx-lh-pericalcarine |       0.758 | 
     1.083… |
| input.rescaled.nii.gz |   6 | ctx-rh-pericalcarine |       0.409 | 
     1.197… |
| input.rescaled.nii.gz |   6 | ctx-lh-pericalcarine |       0.470 | 
     1.058… |
| mgx.ctxgm.nii.gz      |   0 | ctx-rh-pericalcarine |       0.807 | 
     1.007… |
| mgx.ctxgm.nii.gz      |   0 | ctx-lh-pericalcarine |       0.758 | 
     0.888… |
| mgx.ctxgm.nii.gz      |   6 | ctx-rh-pericalcarine |       0.409 | 
     0.915… |
| mgx.ctxgm.nii.gz      |   6 | ctx-lh-pericalcarine |       0.470 | 
     0.809… |


This is using Freesurfer 6.0, and the PET to anatomical registration 
looks fine.


Any ideas why we get such bad values from the GTM method?

Thanks for any help,
Ryan


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Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

[Eckbo, Ryan]

Here's a table with the cerebellum uptake values included -- let me know if you 
need more information.

​ vol   |   psf | roi |   gtmstats_uptake | 
  region_mean
---+---+-+---+---
 input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine| 0.807 |  
1.226
 input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine| 0.758 |  
1.0834
 input.rescaled.nii.gz | 0 | Left-Cerebellum-Cortex  | 0.981 |  
0.994237
 input.rescaled.nii.gz | 0 | Right-Cerebellum-Cortex | 1.019 |  
1.03552
 mgx.ctxgm.nii.gz  | 0 | ctx-rh-pericalcarine| 0.807 |  
1.00685
 mgx.ctxgm.nii.gz  | 0 | ctx-lh-pericalcarine| 0.758 |  
0.887616
 input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine| 0.409 |  
1.19702
 input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine| 0.47  |  
1.05779
 input.rescaled.nii.gz | 6 | Left-Cerebellum-Cortex  | 0.984 |  
0.970736
 input.rescaled.nii.gz | 6 | Right-Cerebellum-Cortex | 1.016 |  
1.01104
 mgx.ctxgm.nii.gz  | 6 | ctx-rh-pericalcarine| 0.409 |  
0.915328
 mgx.ctxgm.nii.gz  | 6 | ctx-lh-pericalcarine| 0.47  |  
0.809017

Thanks!
Ryan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, March 11, 2020 10:01 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

What is the value for cerebellum in those three scenarious (gtm, no pvc, and 
mgx)?

On 3/10/2020 12:37 PM, Eckbo, Ryan wrote:
Hello experts,

I've recently run into a case the gtmstats uptake (reference region: 
cerebellum) for the pericarlcarine ROI's are as low as 0.40,
however computing the voxel wise mean using input.rescaled.nii.gz and 
mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1,
as expected:

| vol   | psf | roi  | gtmstats_uptake | 
mean_uptake |
| - | --- |  | --- | 
--- |
| input.rescaled.nii.gz |   0 | ctx-rh-pericalcarine |   0.807 |  
1.226… |
| input.rescaled.nii.gz |   0 | ctx-lh-pericalcarine |   0.758 |  
1.083… |
| input.rescaled.nii.gz |   6 | ctx-rh-pericalcarine |   0.409 |  
1.197… |
| input.rescaled.nii.gz |   6 | ctx-lh-pericalcarine |   0.470 |  
1.058… |
| mgx.ctxgm.nii.gz  |   0 | ctx-rh-pericalcarine |   0.807 |  
1.007… |
| mgx.ctxgm.nii.gz  |   0 | ctx-lh-pericalcarine |   0.758 |  
0.888… |
| mgx.ctxgm.nii.gz  |   6 | ctx-rh-pericalcarine |   0.409 |  
0.915… |
| mgx.ctxgm.nii.gz  |   6 | ctx-lh-pericalcarine |   0.470 |  
0.809… |

This is using Freesurfer 6.0, and the PET to anatomical registration looks fine.

Any ideas why we get such bad values from the GTM method?

Thanks for any help,
Ryan




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vol,psf,roi,gtmstats_uptake,region_mean
input.rescaled.nii.gz,0,ctx-rh-pericalcarine,0.807,1.2259972095489502
input.rescaled.nii.gz,0,ctx-lh-pericalcarine,0.758,1.083396077156067
input.rescaled.nii.gz,0,Left-Cerebellum-Cortex,0.981,0.9942372441291809
input.rescaled.nii.gz,0,Right-Cerebellum-Cortex,1.0191,1.0355194807052612
mgx.ctxgm.nii.gz,0,ctx-rh-pericalcarine,0.807,1.006852149963379
mgx.ctxgm.nii.gz,0,ctx-lh-pericalcarine,0.758,0.8876161575317383
input.rescaled.nii.gz,6,ctx-rh-pericalcarine,0.409,1.1970176696777344
input.rescaled.nii.gz,6,ctx-lh-pericalcarine,0.47,1.057787299156189
input.rescaled.nii.gz,6,Left-Cerebellum-Cortex,0.9841,0.9707359671592712
input.rescaled.nii.gz,6,Right-Cerebellum-Cortex,1.016,1.0110423564910889
mgx.ctxgm.nii.gz,6,ctx-rh-pericalcarine,0.409,0.9153279066085815
mgx.ctxgm.nii.gz,6,ctx-lh-pericalcarine,0.47,0.8090171217918396
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Re: [Freesurfer] PetSurfer reference region

[Douglas N. Greve]

On 3/24/2020 6:11 PM, Dincer, Aylin wrote:

 External Email - Use Caution

Hello PetSurfer experts,

We found the SUVR values for the reference region (lh/rh cerebellum cortex) 
does not equal 1 in the gtm.stat.dat file.

We tried a few things:
1) leaving the PET image as multi-frames (ref region SUVR about 1.34)
As I mentioned below, don't do it this way if you want the gtm stats to 
have 1 in  the reference region.

2) concatenating the frames as suggested in the previous response (ref region 
SUVR about 1.34)

This was not what what was suggested.

3) running with the SUV image (ref region SUVR about 1.003).
I think this is what I suggested. You have two reference regions (8 and 
47) but you only list one value above. My guess is that the other is 
going to be .997 so that they average to 1


I attached the terminal output and the gtm.stat.dat file from the concatenated 
image run.

Here is the command we ran using v6:
mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf 8--seg 
${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx .01 
--rescale 8 47 -o regmean_gtmpvc_output

Let me know if you have suggestions.

Thanks so much,
Aylin

___

Message: 11
Date: Fri, 6 Mar 2020 16:59:53 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <8c262861-3272-151b-ae18-906898408...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I think the issue is that your input has multiple frames (6). It will
compute the scaling from all 6 whereas the gtm.stats file is only from
the first frame. Try running it with a single frame. Note that the
gtm.nii.gz will have all the frames for each ROI.


On 3/6/2020 3:56 PM, Dincer, Aylin wrote:

  External Email - Use Caution

Thanks for the quick reply. I attached the terminal output to this email. We 
are running this on v6.

Best,
Aylin

___
Message: 9
Date: Fri, 6 Mar 2020 11:50:51 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I cannot replicate this in either v6 or v7beta. Can you send the
terminal output?

On 3/5/2020 1:32 PM, Dincer, Aylin wrote:

External Email - Use Caution

Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but
noticed that the SUVR values for lh/rh cerebellum cortex do not have a
value of 1 (which is what we were expecting). The actual SUVR values
are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
the stats file (gtm.stats.dat) and below is the command we ran.

mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output

Let me know if you need any more details.

Thanks so much,

Aylin



_

Aylin Dincer

Senior Research Technician

NeuroImaging Laboratories

Imaging Core, Benzinger Lab

314-362-3629


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Hello PetSurfer experts,

We found the SUVR values for the reference region (lh/rh cerebellum cortex) 
does not equal 1 in the gtm.stat.dat file.

We tried a few things:
1) leaving the PET image as multi-frames (ref region SUVR about 1.34)
2) concatenating the frames as suggested in the previous response (ref region 
SUVR about 1.34)
3) running with the SUV image (ref region SUVR about 1.003).

I attached the terminal output and the gtm.stat.dat file from the concatenated 
image run.

Here is the command we ran using v6:
mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf 8--seg 
${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx .01 
--rescale 8 47 -o regmean_gtmpvc_output

Let me know if you have suggestions.

Thanks so much,
Aylin

___

Message: 11
Date: Fri, 6 Mar 2020 16:59:53 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <8c262861-3272-151b-ae18-906898408...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I think the issue is that your input has multiple frames (6). It will
compute the scaling from all 6 whereas the gtm.stats file is only from
the first frame. Try running it with a single frame. Note that the
gtm.nii.gz will have all the frames for each ROI.


On 3/6/2020 3:56 PM, Dincer, Aylin wrote:
>  External Email - Use Caution
>
> Thanks for the quick reply. I attached the terminal output to this email. We 
> are running this on v6.
>
> Best,
> Aylin
>
> ___
> Message: 9
> Date: Fri, 6 Mar 2020 11:50:51 -0500
> From: "Douglas N. Greve" 
> Subject: Re: [Freesurfer] PetSurfer reference region
> To: 
> Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> I cannot replicate this in either v6 or v7beta. Can you send the
> terminal output?
>
> On 3/5/2020 1:32 PM, Dincer, Aylin wrote:
>> External Email - Use Caution
>>
>> Hello PetSurfer experts,
>>
>> We are using the cerebellum cortex as our reference region, but
>> noticed that the SUVR values for lh/rh cerebellum cortex do not have a
>> value of 1 (which is what we were expecting). The actual SUVR values
>> are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
>> the stats file (gtm.stats.dat) and below is the command we ran.
>>
>> mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
>> ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
>> PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output
>>
>> Let me know if you need any more details.
>>
>> Thanks so much,
>>
>> Aylin
>>
>> 
>>
>> _
>>
>> Aylin Dincer
>>
>> Senior Research Technician
>>
>> NeuroImaging Laboratories
>>
>> Imaging Core, Benzinger Lab
>>
>> 314-362-3629


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


gtm.stats.dat
Description: gtm.stats.dat


mri_gtmpvc.log
Description: mri_gtmpvc.log
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Re: [Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

[Douglas N. Greve]

What is the value for cerebellum in those three scenarious (gtm, no pvc, 
and mgx)?


On 3/10/2020 12:37 PM, Eckbo, Ryan wrote:

Hello experts,

I've recently run into a case the gtmstats uptake (reference region: 
cerebellum) for the pericarlcarine ROI's are as low as 0.40,
however computing the voxel wise mean using input.rescaled.nii.gz and 
mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1,

as expected:

| vol                 | psf | roi                  | gtmstats_uptake | 
mean_uptake |
| - | --- |  | --- 
| --- |
| input.rescaled.nii.gz |   0 | ctx-rh-pericalcarine |   0.807 |     
 1.226… |
| input.rescaled.nii.gz |   0 | ctx-lh-pericalcarine |   0.758 |     
 1.083… |
| input.rescaled.nii.gz |   6 | ctx-rh-pericalcarine |   0.409 |     
 1.197… |
| input.rescaled.nii.gz |   6 | ctx-lh-pericalcarine |   0.470 |     
 1.058… |
| mgx.ctxgm.nii.gz      |   0 | ctx-rh-pericalcarine |   0.807 |     
 1.007… |
| mgx.ctxgm.nii.gz      |   0 | ctx-lh-pericalcarine |   0.758 |     
 0.888… |
| mgx.ctxgm.nii.gz      |   6 | ctx-rh-pericalcarine |   0.409 |     
 0.915… |
| mgx.ctxgm.nii.gz      |   6 | ctx-lh-pericalcarine |   0.470 |     
 0.809… |


This is using Freesurfer 6.0, and the PET to anatomical registration 
looks fine.


Any ideas why we get such bad values from the GTM method?

Thanks for any help,
Ryan


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[Freesurfer] Petsurfer: Gtmstats < 1, voxel wise mean is fine

[Eckbo, Ryan]

Hello experts,

I've recently run into a case the gtmstats uptake (reference region: 
cerebellum) for the pericarlcarine ROI's are as low as 0.40,
however computing the voxel wise mean using input.rescaled.nii.gz and 
mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1,
as expected:

| vol   | psf | roi  | gtmstats_uptake | 
mean_uptake |
| - | --- |  | --- | 
--- |
| input.rescaled.nii.gz |   0 | ctx-rh-pericalcarine |   0.807 |  
1.226… |
| input.rescaled.nii.gz |   0 | ctx-lh-pericalcarine |   0.758 |  
1.083… |
| input.rescaled.nii.gz |   6 | ctx-rh-pericalcarine |   0.409 |  
1.197… |
| input.rescaled.nii.gz |   6 | ctx-lh-pericalcarine |   0.470 |  
1.058… |
| mgx.ctxgm.nii.gz  |   0 | ctx-rh-pericalcarine |   0.807 |  
1.007… |
| mgx.ctxgm.nii.gz  |   0 | ctx-lh-pericalcarine |   0.758 |  
0.888… |
| mgx.ctxgm.nii.gz  |   6 | ctx-rh-pericalcarine |   0.409 |  
0.915… |
| mgx.ctxgm.nii.gz  |   6 | ctx-lh-pericalcarine |   0.470 |  
0.809… |

This is using Freesurfer 6.0, and the PET to anatomical registration looks fine.

Any ideas why we get such bad values from the GTM method?

Thanks for any help,
Ryan

vol,psf,roi,gtmstats_uptake,mean_uptake
input.rescaled.nii.gz,0,ctx-rh-pericalcarine,0.807,1.2259972095489502
input.rescaled.nii.gz,0,ctx-lh-pericalcarine,0.758,1.083396077156067
input.rescaled.nii.gz,6,ctx-rh-pericalcarine,0.409,1.1970176696777344
input.rescaled.nii.gz,6,ctx-lh-pericalcarine,0.47,1.057787299156189
mgx.ctxgm.nii.gz,0,ctx-rh-pericalcarine,0.807,1.006852149963379
mgx.ctxgm.nii.gz,0,ctx-lh-pericalcarine,0.758,0.8876161575317383
mgx.ctxgm.nii.gz,6,ctx-rh-pericalcarine,0.409,0.9153279066085815
mgx.ctxgm.nii.gz,6,ctx-lh-pericalcarine,0.47,0.8090171217918396
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Re: [Freesurfer] PetSurfer reference region

[Douglas N. Greve]

I think the issue is that your input has multiple frames (6). It will 
compute the scaling from all 6 whereas the gtm.stats file is only from 
the first frame. Try running it with a single frame. Note that the 
gtm.nii.gz will have all the frames for each ROI.



On 3/6/2020 3:56 PM, Dincer, Aylin wrote:

 External Email - Use Caution

Thanks for the quick reply. I attached the terminal output to this email. We 
are running this on v6.

Best,
Aylin

___
Message: 9
Date: Fri, 6 Mar 2020 11:50:51 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I cannot replicate this in either v6 or v7beta. Can you send the
terminal output?

On 3/5/2020 1:32 PM, Dincer, Aylin wrote:

External Email - Use Caution

Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but
noticed that the SUVR values for lh/rh cerebellum cortex do not have a
value of 1 (which is what we were expecting). The actual SUVR values
are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
the stats file (gtm.stats.dat) and below is the command we ran.

mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output

Let me know if you need any more details.

Thanks so much,

Aylin



_

Aylin Dincer

Senior Research Technician

NeuroImaging Laboratories

Imaging Core, Benzinger Lab

314-362-3629



The materials in this message are private and may contain Protected
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you are not the intended recipient, be advised that any unauthorized
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the contents of this information is strictly prohibited. If you have
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Re: [Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Thanks for the quick reply. I attached the terminal output to this email. We 
are running this on v6.

Best,
Aylin

___
Message: 9
Date: Fri, 6 Mar 2020 11:50:51 -0500
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] PetSurfer reference region
To: 
Message-ID: <64d6089e-f818-e30e-deff-98a812b72...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I cannot replicate this in either v6 or v7beta. Can you send the
terminal output?

On 3/5/2020 1:32 PM, Dincer, Aylin wrote:
>
> External Email - Use Caution
>
> Hello PetSurfer experts,
>
> We are using the cerebellum cortex as our reference region, but
> noticed that the SUVR values for lh/rh cerebellum cortex do not have a
> value of 1 (which is what we were expecting). The actual SUVR values
> are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached
> the stats file (gtm.stats.dat) and below is the command we ran.
>
> mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf
> ${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask
> PSF+2 .01 --mgx .01 --rescale 8 47 ?o regmean_gtmpvc_output
>
> Let me know if you need any more details.
>
> Thanks so much,
>
> Aylin
>
> 
>
> _
>
> Aylin Dincer
>
> Senior Research Technician
>
> NeuroImaging Laboratories
>
> Imaging Core, Benzinger Lab
>
> 314-362-3629
>
> 
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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pet_regmiddle_pvc_rerun_2020_03_06.log
Description: pet_regmiddle_pvc_rerun_2020_03_06.log
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Re: [Freesurfer] PetSurfer reference region

[Douglas N. Greve]

I cannot replicate this in either v6 or v7beta. Can you send the 
terminal output?


On 3/5/2020 1:32 PM, Dincer, Aylin wrote:


External Email - Use Caution

Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but 
noticed that the SUVR values for lh/rh cerebellum cortex do not have a 
value of 1 (which is what we were expecting). The actual SUVR values 
are 1.31 for the lh and 1.35 for the rh cerebellum cortex. I attached 
the stats file (gtm.stats.dat) and below is the command we ran.


mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf 
${FWHM} --seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask 
PSF+2 .01 --mgx .01 --rescale 8 47 –o regmean_gtmpvc_output


Let me know if you need any more details.

Thanks so much,

Aylin



_

Aylin Dincer

Senior Research Technician

NeuroImaging Laboratories

Imaging Core, Benzinger Lab

314-362-3629



The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
use, disclosure, copying or the taking of any action in reliance on 
the contents of this information is strictly prohibited. If you have 
received this email in error, please immediately notify the sender via 
telephone or return mail.



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Re: [Freesurfer] petsurfer

[Douglas N. Greve]

I cannot replicate this, eg

In matlab
a = fast_vol2mat(MRIread('gtm.nii.gz'));
a(1:10)
  Columns 1 through 7
    0.7957    1.0565    1.5711    1.7842    1.8625    1.9539 1.2499
  Columns 8 through 10
    1.3188    1.4063    1.2536

From gtm,.stats.dat
  1    2 Left-Cerebral-White-Matter  wm 25583 
10872.101    0.796   0.1501
  2    7 Left-Cerebellum-White-Matter    wm 1472  691.994    
1.057   0.1843
  3    8 Left-Cerebellum-Cortex  subcort_gm 5326 
2833.077    1.571   0.1451
  4   10 Left-Thalamus-Proper    subcort_gm 643  333.888    
1.784   0.1808
  5   11 Left-Caudate    subcort_gm 353  117.232    
1.863   0.1650
  6   12 Left-Putamen    subcort_gm 576  256.726    
1.954   0.1543
  7   13 Left-Pallidum   subcort_gm 146   52.532    
1.250   0.0782
  8   16 Brain-Stem  subcort_gm 1139  
517.830    1.319   0.2061
  9   17 Left-Hippocampus    subcort_gm 477  174.082    
1.406   0.1226
 10   18 Left-Amygdala   subcort_gm 186   65.184    
1.254   0.0847


You can see that the values match




On 3/3/2020 12:39 PM, Laboratorio de Neurociencia Funcional wrote:


External Email - Use Caution

Dear Freesurfer experts,
I have compared the PVC uptake values of gtm.stats with the values of
gtm.nii.gz with the function load_nii in matlab. I noted
that values in matlab are reversed, i. e., the first value in
gtm.stats matches with the last value in gtm.nii.gz and so on.

Could you confirm me that nopvc.nii.gz values are also reversed
when loaded with load_nii in matlab? I have no way to check this.
Thank you in advance.
Best, Marina

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[Freesurfer] PetSurfer reference region

[Dincer, Aylin]

External Email - Use Caution

Hello PetSurfer experts,

We are using the cerebellum cortex as our reference region, but noticed that 
the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is 
what we were expecting). The actual SUVR values are 1.31 for the lh and 1.35 
for the rh cerebellum cortex. I attached the stats file (gtm.stats.dat) and 
below is the command we ran.

mri_gtmpvc --i regmean.nii.gz --reg regmean_template.reg.lta --psf ${FWHM} 
--seg ${MR_ID}/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF+2 .01 --mgx 
.01 --rescale 8 47 -o regmean_gtmpvc_output

Let me know if you need any more details.

Thanks so much,
Aylin



_
Aylin Dincer
Senior Research Technician
NeuroImaging Laboratories
Imaging Core, Benzinger Lab
314-362-3629



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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immediately notify the sender via telephone or return mail.


gtm.stats.dat
Description: gtm.stats.dat
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[Freesurfer] petsurfer

[Laboratorio de Neurociencia Funcional]

External Email - Use Caution

Dear Freesurfer experts,

I have compared the PVC uptake values of gtm.stats with the values of
gtm.nii.gz with the function load_nii in matlab. I noted
that values in matlab are reversed, i. e., the first value in
gtm.stats matches with the last value in gtm.nii.gz and so on.

Could you confirm me that nopvc.nii.gz values are also reversed
when loaded with load_nii in matlab? I have no way to check this.

Thank you in advance.

Best, Marina
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Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you  Dr.Greve.

I applied to rbv.nii.gz volume to anatomical space.

You said, bbpet2anat.lta. using mri_vol2vol

but I tested. registration using bbpet2anat.lta was not correct on native
T1 space.
So I tested rbv2anat.lta for registration. that was okay.

What is difference between SPM coregistration rbv onto orig.mgz and
registration using rbv2anat.lta??

Best regards
Soo
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Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

*Thank you Dr. Greve for your answer*


I checked all about your comment.

I have questions more.

1. I found that volumes or counts in gtm.stats.dat are for native PET
space. If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.

What do you prefer or recommend?

I'm not sure what you are trying to get. voxel volume or SUVR?


*-> Yes. Voxel volume for SUVR analysis.*

*I compared gtm.stats.dat from both GTM and RBV method.*

*They were all same SUVR. I think region masks for gtm and rbv are
same as pvc-masks, arent they?*


2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader

because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.

and you also said, smoothing is required after PVC. (Surface or volume based
smoothing (resonable).

The RBV is in anatomical space, if you want to map it back to pet space, you
need the registration file in the aux folder (not --regheader).

*-> RBV has 0.5mm for voxelsize. even though I put image for input which
has 1mm isotropic volume. *
*You said that 'use in lta file in aux folder'. There are many lta files.
So let me know what it is. *

*- anat2bbpet.lta*
*- anat2rbv.lta*
*- bbpet2anat.lta*
*- bbpet2pet.lta*
*- pet2bbpet.lta*
*- rbv2anat.lta*

*my purpose is this.  I want to map rbv.nii.gz to original T1MR space.
Could you tell me how to do ?*

*Thank you so much, Dr.Greve*
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Re: [Freesurfer] PetSurfer questions

[Douglas N. Greve]

On 2/9/2020 10:19 PM, Soo-Jong Kim wrote:


External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET 
space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is 
available using rbv.nii.gz from mri_gtmpvc,


Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat 
--rescale (reference regions) for SUVR in PET space.

What do you prefer or recommend?

I'm not sure what you are trying to get. voxel volume or SUVR?


2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o 
test.nii --regheader

because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC. (Surface or volume 
based smoothing (resonable).
The RBV is in anatomical space, if you want to map it back to pet space, 
you need the registration file in the aux folder (not --regheader).


Best regards,
Soo

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Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.
What do you prefer or recommend?

2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader
because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC.  (Surface or volume
based smoothing (resonable).

Best regards,
Soo
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Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.
What do you prefer or recommend?

2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader
because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC.  (Surface or volume
based smoothing (resonable).

Best regards,
Soo
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Re: [Freesurfer] PetSurfer questions

[Douglas N. Greve]

On 2/3/2020 11:56 PM, Soo-Jong Kim wrote:


External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET 
space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is 
available using rbv.nii.gz from mri_gtmpvc,


Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat 
--rescale (reference regions) for SUVR in PET space.

What do you prefer or recommend?
I'm not sure why you would use the ROI volume from the PET analysis at 
all. Why not just use the data in the aseg.stats or the ?h.aparc.stats?


2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o 
test.nii --regheader

because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just checked, and the RBV is in the anatomical space and so 
--regheader is not appropriate. if you really want to map it back to the 
pet space, you will need to supply a registration file, but there is 
probably no reason to do this.

I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC. (Surface or volume 
based smoothing (resonable).


Best regards,
S

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Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

Thank you, Dr. Greve

I checked all about your comment.

I have questions more.
1. I found that volumes or counts in gtm.stats.dat are for native PET space.
If co-registered PET onto corresponding MRI(i.e. MRI space) is available
using rbv.nii.gz from mri_gtmpvc,

Or if you recommend it by gtm.stats.dat, I can use gtm.stats.dat --rescale
(reference regions) for SUVR in PET space.
What do you prefer or recommend?

2. I used mri_vol2vol --mov rbv.nii.gz --targ original_PET.nii --o test.nii
--regheader
because rbv.nii.gz is in different space.
but when overlaid with them, registration is not correct.  (WHY)
rbv.nii.gz is in different space, even not in T1.mgz space. (DKT space)
I just wanted to use the pv-corrected image for image processing.
and you also said, smoothing is required after PVC.  (Surface or volume
based smoothing (resonable).

Best regards,
S
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Re: [Freesurfer] PetSurfer questions

[Douglas N. Greve]

On 1/30/2020 3:39 AM, Soo-Jong Kim wrote:


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I ran gtmseg for my partial volume correction

1. but I have a question. What regions are for the detail??
in this option.

mri_gtmpvc --default-seg-merge.

I searched mri_gtmpvc --help
but it is default schema for merging ROIs.
So I wanna know what regions you use as default. for example, in 
FreeSurferLUT. 1000, 1010, etc..


Can you tell me what regions freesurfer uses.
Look  in aux/seg.replace.list. The first column is the id of the segment 
being replaced, the 2nd is the new id
2. In general, After PVC (i.e.MG  or RBV),  Does some 
smoothing kernel apply to pv-corrected images from rbv as rbv.nii.gz?
In general, yes, but if you are going to smooth you have to do it the 
right way, otherwise you are just re-imposing PVEs. for cortex, you 
should map it to the surface and smooth on the surface; for the volume I 
would mask out all except subcortical gray and then smooth within 
subcortical gray. These are described on the PETsurfer page.


If then, how large smoothing kernel?

This is an empirical question


Best,
Soo


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Re: [Freesurfer] PetSurfer questions

[Soo-Jong Kim]

External Email - Use Caution

I ran gtmseg for my partial volume correction

1. but I have a question. What regions are for the detail??
in this option.

mri_gtmpvc --default-seg-merge.

I searched mri_gtmpvc --help
but it is default schema for merging ROIs.
So I wanna know what regions you use as default. for example, in
FreeSurferLUT. 1000, 1010, etc..

Can you tell me what regions freesurfer uses.

2. In general, After PVC (i.e.MG or RBV),  Does some smoothing kernel apply
to pv-corrected images from rbv as rbv.nii.gz?

If then, how large smoothing kernel?

Best,
Soo
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Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation

[Boris Rauchmann]

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Dear Doug,

thank you for your effort. Let me know if you have any updates on this.

Best,
Boris

On Fri, Dec 6, 2019 at 5:45 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Hi Boris, I'll try to get to it today. Unfortunately, I think this is
> going to require a fair amount of effort on my part. When I wrote this part
> of PETsurfer, I just did not make it super flexible.
> doug
>
>
> On 12/5/2019 10:17 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Did you already have the time to look at the logfile? Do you have any
> suggestions how to proceed?
>
> Thank you!
>
> Am 02.12.2019 um 19:18 schrieb Boris Rauchmann 
> :
>
> 
> In this example tried it with only the subcortical segmentations from my
> atlas. Please find the logfile attached. It gives me back: "tissue type is
> not set" but I set it to 2 in the LUT.txt
>
> In principle look the following commands right to you?
>
> xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
> BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>
> gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
> subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>
> Ideally I would have a gtmseg with both, the subcortical and the cortical
> structures, but only the subcortical would also be fine as long as I can
> get  mri_gtmpvc running on it.
>
> Thanks,
> Boris
>
> On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Can you send the log file for each of the gtmseg runs?
>>
>> On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>
>> External Email - Use Caution
>> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical
>> structures.
>> I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
>> for parcellation/segmentation stats.
>>
>> For the PET analysis I have the following problem:
>>
>> If I use this command: gtmseg --s test --o test.mgz --ctab
>> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot
>> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>>
>> It gives me the right regions for subcortical structures but it looks
>> like it uses the standard FS parcellation with my labels for the cortical
>> parcellations (only 93 cortical regions instead of 210).
>>
>> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot
>> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my
>> 210 cortical parcellations but the standard FS subcortical segmentations.
>>
>> How can I use both in one gtmseg so that I can proceed with it doing my
>> PET analysis in PETSurfer? It is not totally clear for me what to merge
>> using xcerebralseg.
>>
>> Thanks a lot!
>>
>> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> It gets the subcortical from apas+head.mgz which gets created along the
>>> way by xcerebralseg. You can create your own with xcerebralseg by
>>> specifying your volume as the mergevol. I think this will work, but I'm
>>> not sure. I'm assuming you've used the GCA to create your own
>>> subcortical seg for the given subject
>>>
>>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > I just realized that the above mentioned command (gtmseg --s XYZ --o
>>> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>>> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
>>> > gives me only the cortical segmentation. Is there any way to also
>>> > include the subcortical segmentation based on my individual atlas? I
>>> > also have an Atlas_subcortex.gca file available.
>>> >
>>> > Best,
>>> > Boris
>>> >
>>> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
>>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>>> >
>>> > There is no cut off for the minimum size. As it gets smaller, the
>>> PVC
>>> > noise amplification will become bigger (it also depends on the
>>> > shape as
>>> > well).
>>> >
>>> > I think the --no-xcerseg is the right way to go now
>>> >
>>> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>>> > >
>>> > > External Email - Use Caution
>>> > >
>>> > > Thank you for your prompt answer - the command worked. This is
>>> the
>>> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
>>> > > What is approximately the smallest possible segment when using
>>> PVC?
>>> > > Also, does the exclusion of extracerebral structures harm? I
>>> > used that
>>> > > flag because it complained:
>>> > >
>>> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot
>>> --ctab
>>> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>>> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
>>> > > but you must indicate whether to use what is there (--no-xcerseg)
>>> > > or create a new one and overwrite what is there (--xcerseg)