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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
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
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Thank you so much!
Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve < dgreve@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 CautionDear 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 listFreesurfer@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/1ldbXA5l0aSQnYH7C0wEIwFvfee15EbrfgVhwBBsIJlrrvG... 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_uSP1k8i4m... < https://secure-web.cisco.com/1btT3SxZw_OzaoCYOZqttacFC6HidGXFGvoHH_uSP1k8i4m... .
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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 < fedediantonio98@gmail.com> ha scritto:
Thank you so much!
Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve < dgreve@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 CautionDear 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 listFreesurfer@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/1txnZJ17EtctgFgKvjVFpa4eJvDydSMWkMRZqLYbm6A2qKz... 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-Cgu... < https://secure-web.cisco.com/1TZZ5-LguqY1kjLdVWbgRzIIMt1eUtKCc0bCXQn4iNu-Cgu... .
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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 fedediantonio98@gmail.com ha scritto:
Thank you so much! Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve <dgreve@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 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 <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>_______________________________________________ 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 <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. 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Federica Di Antonio