External Email - Use Caution
Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you.
Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz aparc.a2009s+aseg.mgz aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Tuesday, February 20, 2024 3:22 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you.
External Email - Use Caution
I think these are not grey matter but cortical parcellation. FSL can output grey matter segmentation but I do not think freesurfer has such an output. In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Tuesday, February 20, 2024 3:22 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Grey Matter Intensities
External Email - Use Caution *Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16ifYTsux0iUNjv1oYt9Hv-c1-WpEkOHYOrBq7h3PWyvvS7... 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/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPK... < https://secure-web.cisco.com/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPK... .
Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 9:45 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution I think these are not grey matter but cortical parcellation. FSL can output grey matter segmentation but I do not think freesurfer has such an output. In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz aparc.a2009s+aseg.mgz aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Tuesday, February 20, 2024 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/16ifYTsux0iUNjv1oYt9Hv-c1-WpEkOHYOrBq7h3PWyvvS76iScX_WZ2o8lNEaIpa7qoiyDGPhAqI6bC1dHM7bd_Vk_eG55Dj2LfAA0w8W1JH8Gxa-FPjNttxVj00sCJD7OFiTODAbS8thnuOjDATFw5xNSzFI49sqFFsPcZvcQxUGdb7i6Ug8FwqPnD1lh7oyCqLgB_SKeSCqspHSLCW3-OInKWuEem9SSGwzsb96fKTAIdbRUvkhjdxzPv1EG32Xp7e3DkEiGrk6rTPtRmfUU3pz19N6hdnDR6ZEF4Gacf-Gg6hHit5L3yfilTeIqwI_OsthS_zeC-UAbknjzsMcw/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/compliancelinehttps://secure-web.cisco.com/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPKtFwVANxqxacQ7bR2mnKJXiVOVyC22CAWRx3hgqs03JfW_2QI1ZPYeC7kvWHyC5TlXQCqkTEApMINRVVZL-0A3g2fxKAScZFVIqujSq6E8xyG9tbP_M4ket6b5Voe6yxSyy-DBcbedcebX5XctsFWYQmWOUujnVYPWD5ulUfnNCXEA2dk6TVO2twzH8PU-lMQcbsh5yipQjZUnfMF8OuVackAnFHpHtr2W_jPc3gp82Igdnj30WodE71rS5PvIsHvYlbY-MTO5eXzsP2aJRnfBMrCzSWZ3z9lNFYLYUwQ/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/compliancelinehttps://secure-web.cisco.com/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPKtFwVANxqxacQ7bR2mnKJXiVOVyC22CAWRx3hgqs03JfW_2QI1ZPYeC7kvWHyC5TlXQCqkTEApMINRVVZL-0A3g2fxKAScZFVIqujSq6E8xyG9tbP_M4ket6b5Voe6yxSyy-DBcbedcebX5XctsFWYQmWOUujnVYPWD5ulUfnNCXEA2dk6TVO2twzH8PU-lMQcbsh5yipQjZUnfMF8OuVackAnFHpHtr2W_jPc3gp82Igdnj30WodE71rS5PvIsHvYlbY-MTO5eXzsP2aJRnfBMrCzSWZ3z9lNFYLYUwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
External Email - Use Caution
Yes, please That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD BFISCHL@mgh.harvard.edu wrote:
Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Wednesday, February 21, 2024 9:45 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution *I think these are not grey matter but cortical parcellation.
FSL can output grey matter segmentation but I do not think freesurfer has such an output.
In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Tuesday, February 20, 2024 3:22 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Grey Matter Intensities
External Email - Use Caution *Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you.
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/1UXNewDL0uEHZDvbqpxFtennth614SLbFzdgsBGav0taydq... https://secure-web.cisco.com/16ifYTsux0iUNjv1oYt9Hv-c1-WpEkOHYOrBq7h3PWyvvS76iScX_WZ2o8lNEaIpa7qoiyDGPhAqI6bC1dHM7bd_Vk_eG55Dj2LfAA0w8W1JH8Gxa-FPjNttxVj00sCJD7OFiTODAbS8thnuOjDATFw5xNSzFI49sqFFsPcZvcQxUGdb7i6Ug8FwqPnD1lh7oyCqLgB_SKeSCqspHSLCW3-OInKWuEem9SSGwzsb96fKTAIdbRUvkhjdxzPv1EG32Xp7e3DkEiGrk6rTPtRmfUU3pz19N6hdnDR6ZEF4Gacf-Gg6hHit5L3yfilTeIqwI_OsthS_zeC-UAbknjzsMcw/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/1V9NioPMXc9axn43oM3mW2KTLBgJx5O6forHFMt1jYRQOFn... https://secure-web.cisco.com/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPKtFwVANxqxacQ7bR2mnKJXiVOVyC22CAWRx3hgqs03JfW_2QI1ZPYeC7kvWHyC5TlXQCqkTEApMINRVVZL-0A3g2fxKAScZFVIqujSq6E8xyG9tbP_M4ket6b5Voe6yxSyy-DBcbedcebX5XctsFWYQmWOUujnVYPWD5ulUfnNCXEA2dk6TVO2twzH8PU-lMQcbsh5yipQjZUnfMF8OuVackAnFHpHtr2W_jPc3gp82Igdnj30WodE71rS5PvIsHvYlbY-MTO5eXzsP2aJRnfBMrCzSWZ3z9lNFYLYUwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1V9NioPMXc9axn43oM3mW2KTLBgJx5O6forHFMt1jYRQOFn... https://secure-web.cisco.com/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPKtFwVANxqxacQ7bR2mnKJXiVOVyC22CAWRx3hgqs03JfW_2QI1ZPYeC7kvWHyC5TlXQCqkTEApMINRVVZL-0A3g2fxKAScZFVIqujSq6E8xyG9tbP_M4ket6b5Voe6yxSyy-DBcbedcebX5XctsFWYQmWOUujnVYPWD5ulUfnNCXEA2dk6TVO2twzH8PU-lMQcbsh5yipQjZUnfMF8OuVackAnFHpHtr2W_jPc3gp82Igdnj30WodE71rS5PvIsHvYlbY-MTO5eXzsP2aJRnfBMrCzSWZ3z9lNFYLYUwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1UXNewDL0uEHZDvbqpxFtennth614SLbFzdgsBGav0taydq... 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/1V9NioPMXc9axn43oM3mW2KTLBgJx5O6forHFMt1jYRQOFn... < https://secure-web.cisco.com/1V9NioPMXc9axn43oM3mW2KTLBgJx5O6forHFMt1jYRQOFn... .
I think that is exactly one of the outputs of mri_segstats. Check the help on it and see if it does what you want. I believe it is also run by default during recon-all and the values placed into one of the stats output files
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 11:14 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Yes, please That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 9:45 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution I think these are not grey matter but cortical parcellation. FSL can output grey matter segmentation but I do not think freesurfer has such an output. In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz aparc.a2009s+aseg.mgz aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Tuesday, February 20, 2024 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/16ifYTsux0iUNjv1oYt9Hv-c1-WpEkOHYOrBq7h3PWyvvS76iScX_WZ2o8lNEaIpa7qoiyDGPhAqI6bC1dHM7bd_Vk_eG55Dj2LfAA0w8W1JH8Gxa-FPjNttxVj00sCJD7OFiTODAbS8thnuOjDATFw5xNSzFI49sqFFsPcZvcQxUGdb7i6Ug8FwqPnD1lh7oyCqLgB_SKeSCqspHSLCW3-OInKWuEem9SSGwzsb96fKTAIdbRUvkhjdxzPv1EG32Xp7e3DkEiGrk6rTPtRmfUU3pz19N6hdnDR6ZEF4Gacf-Gg6hHit5L3yfilTeIqwI_OsthS_zeC-UAbknjzsMcw/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/compliancelinehttps://secure-web.cisco.com/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPKtFwVANxqxacQ7bR2mnKJXiVOVyC22CAWRx3hgqs03JfW_2QI1ZPYeC7kvWHyC5TlXQCqkTEApMINRVVZL-0A3g2fxKAScZFVIqujSq6E8xyG9tbP_M4ket6b5Voe6yxSyy-DBcbedcebX5XctsFWYQmWOUujnVYPWD5ulUfnNCXEA2dk6TVO2twzH8PU-lMQcbsh5yipQjZUnfMF8OuVackAnFHpHtr2W_jPc3gp82Igdnj30WodE71rS5PvIsHvYlbY-MTO5eXzsP2aJRnfBMrCzSWZ3z9lNFYLYUwQ/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/compliancelinehttps://secure-web.cisco.com/1q-BrgHL_vb8xjTASQUhIwoXdAJz5Qyfc6GaWd77uKoUfPKtFwVANxqxacQ7bR2mnKJXiVOVyC22CAWRx3hgqs03JfW_2QI1ZPYeC7kvWHyC5TlXQCqkTEApMINRVVZL-0A3g2fxKAScZFVIqujSq6E8xyG9tbP_M4ket6b5Voe6yxSyy-DBcbedcebX5XctsFWYQmWOUujnVYPWD5ulUfnNCXEA2dk6TVO2twzH8PU-lMQcbsh5yipQjZUnfMF8OuVackAnFHpHtr2W_jPc3gp82Igdnj30WodE71rS5PvIsHvYlbY-MTO5eXzsP2aJRnfBMrCzSWZ3z9lNFYLYUwQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/1UXNewDL0uEHZDvbqpxFtennth614SLbFzdgsBGav0taydqcybBj4G8q7GjHQnREl56uawoYrjID8Jqk2000XIbLcEWFDatPdylmyz2uN2aH1siCACWW6evLBvQosxCRDhWf6ZS9WUg5FamyE7GUKXITd6VfSlgnYpiLwIXHKGPbMVBZ2RaYK1LgrX2bx0ouuSkZx1VK43tbwRuEjy32XqvzyazVrvuWbRJv44rfP1gutOpq7QktNlU9gHOrN0B7oCafyrg28zQ-aS8DPWdEbCxuDYPRp-gwnPOaYkPEoP94EKEi-FqDh4op7BxY-sIlR/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/compliancelinehttps://secure-web.cisco.com/1V9NioPMXc9axn43oM3mW2KTLBgJx5O6forHFMt1jYRQOFnI-o49PLQHU2tyqaY2_qpY_h0J-0ka2oWJMgaqgs_93Qp-h_yhZFHw0MZvpdm-b06qa0eMAphaE4ie3YadZD6otTgtJQsBroroAHuwNYQ3UXsSIxkboDUBf0ZbwQYRylDAlJ6OsWQdMH_aKCRY1svYqkxDSuCFuBwBJ0ITJEURRr_wHSYfIBbeyEHJ2byoN401K6fzxgoKbe6LUxH4kuTk02vLPQDJVfQwYaFVtrynRslt3TwVLtzSDyKwtdTpGAsDPV4hv6Co4a89Ss_fX/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/compliancelinehttps://secure-web.cisco.com/1V9NioPMXc9axn43oM3mW2KTLBgJx5O6forHFMt1jYRQOFnI-o49PLQHU2tyqaY2_qpY_h0J-0ka2oWJMgaqgs_93Qp-h_yhZFHw0MZvpdm-b06qa0eMAphaE4ie3YadZD6otTgtJQsBroroAHuwNYQ3UXsSIxkboDUBf0ZbwQYRylDAlJ6OsWQdMH_aKCRY1svYqkxDSuCFuBwBJ0ITJEURRr_wHSYfIBbeyEHJ2byoN401K6fzxgoKbe6LUxH4kuTk02vLPQDJVfQwYaFVtrynRslt3TwVLtzSDyKwtdTpGAsDPV4hv6Co4a89Ss_fX/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
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There is no such flag in mri_segstats to calculate gray matter cortical parcels. There is a flag for total gray matter rather. Nevertheless, I think there is a file in recon-all output that has white matter to gray matter ratio : lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I may be able to create a code to calculate the gray matter.
On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> wrote:
I think that is exactly one of the outputs of mri_segstats. Check the help on it and see if it does what you want. I believe it is also run by default during recon-all and the values placed into one of the stats output files
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Wednesday, February 21, 2024 11:14 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution *Yes, please
That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> wrote:
Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Wednesday, February 21, 2024 9:45 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution *I think these are not grey matter but cortical parcellation.
FSL can output grey matter segmentation but I do not think freesurfer has such an output.
In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Tuesday, February 20, 2024 3:22 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Grey Matter Intensities
External Email - Use Caution *Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you.
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I guess I still don’t understand what you want. Is it a single number for all gray matter over the entire brain? Or broken down by structure/parcel?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 12:52 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution There is no such flag in mri_segstats to calculate gray matter cortical parcels. There is a flag for total gray matter rather. Nevertheless, I think there is a file in recon-all output that has white matter to gray matter ratio : lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I may be able to create a code to calculate the gray matter.
On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: I think that is exactly one of the outputs of mri_segstats. Check the help on it and see if it does what you want. I believe it is also run by default during recon-all and the values placed into one of the stats output files
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 11:14 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Yes, please That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 9:45 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution I think these are not grey matter but cortical parcellation. FSL can output grey matter segmentation but I do not think freesurfer has such an output. In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz aparc.a2009s+aseg.mgz aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Tuesday, February 20, 2024 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
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External Email - Use Caution
There is a single number for all the gray matter over the entire brain. They are not broken down into structures or parcel unless it is only in the aseg (subcortical parcellation). I have found a way to calculate it. Now, I wanna write this lh.w-g.pct in the stats folder into a table. It contains the ratio of white matter to gray matter intensity. Is there some way to do that? There is aparcstats2table to read aparcstats and asegstats2table to read aseg stats. Is there a function to read the lh.w-g.pct or rh.w-g.pct stats?
On Wed, Feb 21, 2024 at 8:57 PM Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> wrote:
I guess I still don’t understand what you want. Is it a single number for all gray matter over the entire brain? Or broken down by structure/parcel?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Wednesday, February 21, 2024 12:52 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution *There is no such flag in mri_segstats to calculate gray matter cortical parcels. There is a flag for total gray matter rather. Nevertheless, I think there is a file in recon-all output that has white matter to gray matter ratio : lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I may be able to create a code to calculate the gray matter.
On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> wrote:
I think that is exactly one of the outputs of mri_segstats. Check the help on it and see if it does what you want. I believe it is also run by default during recon-all and the values placed into one of the stats output files
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Wednesday, February 21, 2024 11:14 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution *Yes, please
That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD < BFISCHL@mgh.harvard.edu> wrote:
Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Wednesday, February 21, 2024 9:45 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution *I think these are not grey matter but cortical parcellation.
FSL can output grey matter segmentation but I do not think freesurfer has such an output.
In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI *Sent:* Tuesday, February 20, 2024 3:22 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Grey Matter Intensities
External Email - Use Caution *Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
Thank you.
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How about this command:
mri_segstats --seg $FREESURFER_HOME/subjects/bert/mri/aparc+aseg.mgz --i $FREESURFER_HOME/subjects/bert/mri/orig.mgz --sum bert-orig.aparc+aseg.sum
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 12:52 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution There is no such flag in mri_segstats to calculate gray matter cortical parcels. There is a flag for total gray matter rather. Nevertheless, I think there is a file in recon-all output that has white matter to gray matter ratio : lh.w-g.pct and rh.w-g.pct and I have a file for the white matter so I think I may be able to create a code to calculate the gray matter.
On Wed, Feb 21, 2024 at 7:21 PM Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: I think that is exactly one of the outputs of mri_segstats. Check the help on it and see if it does what you want. I believe it is also run by default during recon-all and the values placed into one of the stats output files
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 11:14 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Yes, please That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> wrote: Can you clarify what you mean by “measure the intensities for the grey matter regions”? You could for example compute the mean gray matter intensity within each cortical parcel and each subcortical structure. Is that what you want?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Wednesday, February 21, 2024 9:45 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Grey Matter Intensities
External Email - Use Caution I think these are not grey matter but cortical parcellation. FSL can output grey matter segmentation but I do not think freesurfer has such an output. In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no intensity measure. I want to know how I can measure the intensities for the grey matter regions.
On Wed, Feb 21, 2024, 5:25 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz aparc.a2009s+aseg.mgz aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg volume.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ERNEST KISSI Sent: Tuesday, February 20, 2024 3:22 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Grey Matter Intensities
External Email - Use Caution Hi Freesurfer team,
Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional grey matter intensities.
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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/compliancelinehttps://secure-web.cisco.com/1IFOMg9iLDng8jO3RJYfHBr6EEwI0sI9K2MTEcG2WNY5xWFCkwTyBjLSTbcpX0MB3PPtisFuEPXacJZlGERsxLeI5boPvchzC6iH843V3vz4c2jJqPyGyX4uBt7NLCHcsjSzJ2yLUvmEgEAugccxVwsNKu8UY0x69pis9gWhZdagfXi4AMbgmgtmLE1PalZ8--UgnCOO1RT0K3ZMaRYo7KHt7V9Fuo53A4L6EnGe1Scgi9fme5BqqbG-PBZkFzDP4EBe71UQSDlFwogAV9uOGXNMVR_ZCj-MbQDiRjFmrCzyJf-GS9UgJ2BjKWagkZChu/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/compliancelinehttps://secure-web.cisco.com/1IFOMg9iLDng8jO3RJYfHBr6EEwI0sI9K2MTEcG2WNY5xWFCkwTyBjLSTbcpX0MB3PPtisFuEPXacJZlGERsxLeI5boPvchzC6iH843V3vz4c2jJqPyGyX4uBt7NLCHcsjSzJ2yLUvmEgEAugccxVwsNKu8UY0x69pis9gWhZdagfXi4AMbgmgtmLE1PalZ8--UgnCOO1RT0K3ZMaRYo7KHt7V9Fuo53A4L6EnGe1Scgi9fme5BqqbG-PBZkFzDP4EBe71UQSDlFwogAV9uOGXNMVR_ZCj-MbQDiRjFmrCzyJf-GS9UgJ2BjKWagkZChu/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
freesurfer@nmr.mgh.harvard.edu
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ERNEST KISSI -
Fischl, Bruce R.,PHD -
Huang, Yujing