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Dear experts,
I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer.
Do you think this error can result from previous errors in the analysis? Or is it in some way plausible?
Thank you for your patience, Federica
can you send an example?
On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
External Email - Use Caution
Dear experts,
I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer.
Do you think this error can result from previous errors in the analysis? Or is it in some way plausible?
Thank you for your patience, Federica
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
of course: I run the same line of command for both amyloid and tau pet images with a fwhm = 1 in order to see what have happened
mri_gtmpvc --i taupet.nii --reg tau.reg.lta --psf 1 --seg gtmseg.mgz --auto-mask 1 .01 --mgx .01 --no-rescale --o tau.output
mri_gtmpvc --i amypet.nii --reg amy.reg.lta --psf 1 --seg gtmseg.mgz --auto-mask 1 .01 --mgx .01 --no-rescale --o amy.output
when I extract gtm.stats.dat file and I compare the number of voxels for the same regions (and for the same subject of course) I obtain these values (attached files). Can I suppose this effect descends from the flag --automask? maybe the different automatic masks lead to different pixel size.. I don't know, I would be very grateful for any information. Thanks for all the help you can give me about; sincere greetings from
Federica Di Antonio
Il giorno lun 6 mar 2023 alle ore 16:31 Douglas N. Greve < dgreve@mgh.harvard.edu> ha scritto:
can you send an example?
On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
External Email - Use CautionDear experts,
I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer.
Do you think this error can result from previous errors in the analysis? Or is it in some way plausible?
Thank you 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/1VM0gR7PtCdMPFYb3L3zfpgwLUWOX8ubtu2o8dbtq5I-tn9... 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/1x7rDMr7odbpYAD4E4Mm3_G0LekUdeH2QliAm_KNo9VP1-c... < https://secure-web.cisco.com/1x7rDMr7odbpYAD4E4Mm3_G0LekUdeH2QliAm_KNo9VP1-c... .
Do the two inputs have different voxel sizes? The gtm.stats.dat file reports the number of voxels so if the volumes have different voxels sizes, you will get different values out. If this is not the source of the problem, please send the gtm.stats files.
On 3/15/2023 4:06 AM, Federica Di Antonio wrote:
External Email - Use Caution
of course: I run the same line of command for both amyloid and tau pet images with a fwhm = 1 in order to see what have happened
mri_gtmpvc --i taupet.nii --reg tau.reg.lta --psf 1 --seg gtmseg.mgz --auto-mask 1 .01 --mgx .01 --no-rescale --o tau.output
mri_gtmpvc --i amypet.nii --reg amy.reg.lta --psf 1 --seg gtmseg.mgz --auto-mask 1 .01 --mgx .01 --no-rescale --o amy.output
when I extract gtm.stats.dat file and I compare the number of voxels for the same regions (and for the same subject of course) I obtain these values (attached files). Can I suppose this effect descends from the flag --automask? maybe the different automatic masks lead to different pixel size.. I don't know, I would be very grateful for any information. Thanks for all the help you can give me about; sincere greetings from
Federica Di Antonio
Il giorno lun 6 mar 2023 alle ore 16:31 Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
can you send an example? On 2/17/2023 9:38 AM, Federica Di Antonio wrote:External Email - Use Caution Dear experts, I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer. Do you think this error can result from previous errors in the analysis? Or is it in some way plausible? Thank you 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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1VM0gR7PtCdMPFYb3L3zfpgwLUWOX8ubtu2o8dbtq5I-tn9z-7soFv7DH5K8EI2bXLuPaSVv-pYMQyZnsgcedSe6v2dFI-gCGF9h2Pl5k2HHdfHuFVvttvbYCB76-RfjeonptcGdckMyjrR8SivpZwLeVolohwCwWZuRbVLqgtfPXyNBBkrwyTDkwo4ThVWyeycvGN3ROzwz78sna6jOLJAV7L2V2cZ_knNVHqjIenDjW28q83rww6CROiF8mnX5LuD30GsESQSdqjAcCfMoPObkHj-ODhSRDT6MNa_M8GC1Uz09z6sW1mJL3O6wcHqLrXjH9W3lj8VzbmxusyxirqA/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://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1VM0gR7PtCdMPFYb3L3zfpgwLUWOX8ubtu2o8dbtq5I-tn9z-7soFv7DH5K8EI2bXLuPaSVv-pYMQyZnsgcedSe6v2dFI-gCGF9h2Pl5k2HHdfHuFVvttvbYCB76-RfjeonptcGdckMyjrR8SivpZwLeVolohwCwWZuRbVLqgtfPXyNBBkrwyTDkwo4ThVWyeycvGN3ROzwz78sna6jOLJAV7L2V2cZ_knNVHqjIenDjW28q83rww6CROiF8mnX5LuD30GsESQSdqjAcCfMoPObkHj-ODhSRDT6MNa_M8GC1Uz09z6sW1mJL3O6wcHqLrXjH9W3lj8VzbmxusyxirqA/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://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1x7rDMr7odbpYAD4E4Mm3_G0LekUdeH2QliAm_KNo9VP1-c7w5EFJLRth_aZQxbg2piPt0DZaGdpQOHxJBaZWoW3MbOOZXGZOC-pgYljldgaALriyAdJPC7jrdT_xfXQOZQZ_gu39akDgJp2bLuLgeLCW5NeswI-vLZQ-7QeWTKHAsxArzI_aohlxArk4mHLvMfUPgw8ukGgwWGPf2gps01jU9n6SbFkkDgXfhnB7eaFMW-6ZPBKsR58z5HuUr6U-qeUdjoJ2z21OZn0w42wWhsnA4hr6aQOzCGbQRFY6I_vIq_lq0qhYinsvaSFS5cdesoSew_LdDm1VfyhC6giPZw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1x7rDMr7odbpYAD4E4Mm3_G0LekUdeH2QliAm_KNo9VP1-c7w5EFJLRth_aZQxbg2piPt0DZaGdpQOHxJBaZWoW3MbOOZXGZOC-pgYljldgaALriyAdJPC7jrdT_xfXQOZQZ_gu39akDgJp2bLuLgeLCW5NeswI-vLZQ-7QeWTKHAsxArzI_aohlxArk4mHLvMfUPgw8ukGgwWGPf2gps01jU9n6SbFkkDgXfhnB7eaFMW-6ZPBKsR58z5HuUr6U-qeUdjoJ2z21OZn0w42wWhsnA4hr6aQOzCGbQRFY6I_vIq_lq0qhYinsvaSFS5cdesoSew_LdDm1VfyhC6giPZw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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That's right! tau PET images has z voxel dimension that is the double of amy PET voxel.
Thank you so much!
Il giorno lun 27 mar 2023 alle ore 15:49 Douglas N. Greve < dgreve@mgh.harvard.edu> ha scritto:
Do the two inputs have different voxel sizes? The gtm.stats.dat file reports the number of voxels so if the volumes have different voxels sizes, you will get different values out. If this is not the source of the problem, please send the gtm.stats files.
On 3/15/2023 4:06 AM, Federica Di Antonio wrote:
External Email - Use Cautionof course: I run the same line of command for both amyloid and tau pet images with a fwhm = 1 in order to see what have happened
mri_gtmpvc --i taupet.nii --reg tau.reg.lta --psf 1 --seg gtmseg.mgz --auto-mask 1 .01 --mgx .01 --no-rescale --o tau.output
mri_gtmpvc --i amypet.nii --reg amy.reg.lta --psf 1 --seg gtmseg.mgz --auto-mask 1 .01 --mgx .01 --no-rescale --o amy.output
when I extract gtm.stats.dat file and I compare the number of voxels for the same regions (and for the same subject of course) I obtain these values (attached files). Can I suppose this effect descends from the flag --automask? maybe the different automatic masks lead to different pixel size.. I don't know, I would be very grateful for any information. Thanks for all the help you can give me about; sincere greetings from
Federica Di Antonio
Il giorno lun 6 mar 2023 alle ore 16:31 Douglas N. Greve < dgreve@mgh.harvard.edu> ha scritto:
can you send an example?
On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
External Email - Use CautionDear experts,
I hope this email finds you well. I run the pvc correction with mri_gtmpvc for subjects data obtained with two different PET tracers. In gtm.stats.dat, for every subject and every region, the number of voxels evaluated for amyloid tracer is approximately twice the volume evaluated for the second tracer. I'd expect that the volume of a region for the same subject doesn't change with the tracer.
Do you think this error can result from previous errors in the analysis? Or is it in some way plausible?
Thank you for your patience, Federica
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1qjSUA20UaLIh48sCqDL8IPFCPaVkwkYw1aWYFTFe37DxiJ... https://secure-web.cisco.com/1VM0gR7PtCdMPFYb3L3zfpgwLUWOX8ubtu2o8dbtq5I-tn9z-7soFv7DH5K8EI2bXLuPaSVv-pYMQyZnsgcedSe6v2dFI-gCGF9h2Pl5k2HHdfHuFVvttvbYCB76-RfjeonptcGdckMyjrR8SivpZwLeVolohwCwWZuRbVLqgtfPXyNBBkrwyTDkwo4ThVWyeycvGN3ROzwz78sna6jOLJAV7L2V2cZ_knNVHqjIenDjW28q83rww6CROiF8mnX5LuD30GsESQSdqjAcCfMoPObkHj-ODhSRDT6MNa_M8GC1Uz09z6sW1mJL3O6wcHqLrXjH9W3lj8VzbmxusyxirqA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Douglas N. Greve -
Federica Di Antonio