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

2023-05-08 Thread 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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*

https://secure-web.cisco.com/1_MywvR8_zolMkOcnafLXK2HECKPmyW9WeN0YpzqEsAESozHhv1bIZhYFpjq5ofmqHbEInAjdqR5UodNt93sDPw59bt-BPg-dCrEtd3V7UbaGSjaDD1gGyLf-aKKk3iZxuHr2mKRuXjXXwtCLIRC80ohkdJj_c9f8ZdHtSfbcTSmHE0Jb5AC24XCUGEcmVqaQQ-R5pFZX_uF6yoSyrFQH4KAVqi0zhWzSK_BCFMPRaqYj2mxwqsVTU6MxrJA-ldMw0NSKImaz44uNiTZ8HBwkyQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
  



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*

https://secure-web.cisco.com/1_MywvR8_zolMkOcnafLXK2HECKPmyW9WeN0YpzqEsAESozHhv1bIZhYFpjq5ofmqHbEInAjdqR5UodNt93sDPw59bt-BPg-dCrEtd3V7UbaGSjaDD1gGyLf-aKKk3iZxuHr2mKRuXjXXwtCLIRC80ohkdJj_c9f8ZdHtSfbcTSmHE0Jb5AC24XCUGEcmVqaQQ-R5pFZX_uF6yoSyrFQH4KAVqi0zhWzSK_BCFMPRaqYj2mxwqsVTU6MxrJA-ldMw0NSKImaz44uNiTZ8HBwkyQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer


The information in this e-mail is intended only for the person
to whom it is addressed.  If you believe this e-mail was sent
to you in error and the e-mail contains patient information,
please contact the Mass General Brigham Compliance HelpLine at
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*

https://secure-web.cisco.com/1Ai2zY6oId29zKMCRDDB1ScXS3AkDTK-JWwPw6SeD3cOEKz-UXtrBAYQud1k94qAJj4MDTD60lTucCYjCE4Cbep07wjAv7zHX3WTe9jN7B9fjaO-pS89QigCIYsE3-OAlpJtBxKEtuM5UCmiXJTnKlBf2Wi2j5V6PkdD5aCwflGqWt4AGh944Q3a_NoIMT31azIh6GaiJ919BncliK3ohfyzUWmP9VvVtaqjWvl_Zx5J1SMc-iMJ0PWmEiE7kyg9Z-HBtfGMhqaFiy50XsccuAw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline

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

2023-05-08 Thread 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
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/1txnZJ17EtctgFgKvjVFpa4eJvDydSMWkMRZqLYbm6A2qKzj1y2cmw2X7lPmaI0kKSR1DypsiQw9wStJqFJWAk3QBQGG3NukCG4o2ymopSOytNpHe-D44tnrb3Q7vDJpHjD1uzGOCgLM8oxI3i8nmSfM1wG-425Z4G6pd38GLzdq8O6LKMjbVM5JzgJ1iam6SnhcEPmHwTa_k8hX22S6UdOB_fQ_3yhF-ftCNoU81Do3UVTHJew_dFGoPitBp2FrI3L0WL-2SfjVGS_KmFw--EnpQ5XQ89918wTo0S43Algokfn5vFI3m1ith9VNDYM7PnaGqwemW-Ry1aA0EbXqwpQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> The information in this e-mail is intended only for the person to whom it
>> is addressed.  If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at
>> https://secure-web.cisco.com/1TZZ5-LguqY1kjLdVWbgRzIIMt1eUtKCc0bCXQn4iNu-CguFeOzu8AcxkD3DqkROwVR8TSv5pnOW7GGs7RWj9gQz7VnvsMXNfHQEaLcyFrsDwBaSkIs4o0mEuuqOJ-juazmgvtvgO9Yi67suKeP0gp6v6xdjY47XS6IM1vdXCcFxigDJObdp-UOu1CXiEPGj95bWlnveSUwJGAOBrMfPjzHv3tOKH_BOVj14blt3ekk1qwI3pt4Ma0Va05k8zdYqD-Zum2SP4xUoSWgg1tmPpW4vMznpi-Q6pjtUnKuSSXTbSLAAG_HN0oFCV0XVD2VwvkL16SWnDXK2ZXadLhlNShQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>  <
>> https://secure-web.cisco.com/1TZZ5-LguqY1kjLdVWbgRzIIMt1eUtKCc0bCXQn4iNu-CguFeOzu8AcxkD3DqkROwVR8TSv5pnOW7GGs7RWj9gQz7VnvsMXNfHQEaLcyFrsDwBaSkIs4o0mEuuqOJ-juazmgvtvgO9Yi67suKeP0gp6v6xdjY47XS6IM1vdXCcFxigDJObdp-UOu1CXiEPGj95bWlnveSUwJGAOBrMfPjzHv3tOKH_BOVj14blt3ekk1qwI3pt4Ma0Va05k8zdYqD-Zum2SP4xUoSWgg1tmPpW4vMznpi-Q6pjtUnKuSSXTbSLAAG_HN0oFCV0XVD2VwvkL16SWnDXK2ZXadLhlNShQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>>  .
>>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

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

2023-02-27 Thread 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
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1ldbXA5l0aSQnYH7C0wEIwFvfee15EbrfgVhwBBsIJlrrvGp8sQaKyKOI_waamNusIL_773bpJzfb4E9gC7Knd8SeNNxO8oOiSYUzUJTB5iKHoLtH31qoXZHRaQeh-0OtN2TsoU4zz8UzfYlovqcvzL8K1gJ1_I6R2b7hqIwTh7jh2by8ULOUbMfFrKhFCAocHABdMJsjFuJAShAkVenGOJ30fviVXdHrEbXddtvNFpip39mI-gW0xoOxEDOATI4foUQdrJTkvNdFVmBZM62ZUH9uqlhNtqwBQM-BudDMZ4CVGaQWxDWu31raOV_vJyyUyefJOJ-vTa48o91kX960Qw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1btT3SxZw_OzaoCYOZqttacFC6HidGXFGvoHH_uSP1k8i4mmCMYsiYkvg9R_KAQTKAdm2hZ0LhPs1o3eLBDyJ-R5NSpbliuE1Xpb3UhwacpluLSFRURPKSHYM7GtGwCRCcXu_MhWGtk46aFlTtImaaYAGuOMVvykGao-gK3dVUgaWWVyOaduJBUwIW11GP7Ze-LDklYRIim1wMpWGj5aRWSKGnvaT0pOjecotU6faMpTqzObFMAguX7iJnScmX6eq3ex63pe_hadnpIWrtawaFnj3CTq9Fa7m2j-i7ZOk_jgD-RPPTuLFc9uDRrReRiC1wZ7tJhm9FkLRI78dG4TiXw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1btT3SxZw_OzaoCYOZqttacFC6HidGXFGvoHH_uSP1k8i4mmCMYsiYkvg9R_KAQTKAdm2hZ0LhPs1o3eLBDyJ-R5NSpbliuE1Xpb3UhwacpluLSFRURPKSHYM7GtGwCRCcXu_MhWGtk46aFlTtImaaYAGuOMVvykGao-gK3dVUgaWWVyOaduJBUwIW11GP7Ze-LDklYRIim1wMpWGj5aRWSKGnvaT0pOjecotU6faMpTqzObFMAguX7iJnScmX6eq3ex63pe_hadnpIWrtawaFnj3CTq9Fa7m2j-i7ZOk_jgD-RPPTuLFc9uDRrReRiC1wZ7tJhm9FkLRI78dG4TiXw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

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

2022-12-15 Thread 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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.