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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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
<yhuan...@mgh.harvard.edu<mailto:yhuan...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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<mailto: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/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/complianceline<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://www.massgeneralbrigham.org/complianceline<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<mailto: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/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/complianceline<https://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/complianceline<https://secure-web.cisco.com/1V9NioPMXc9axn43oM3mW2KTLBgJx5O6forHFMt1jYRQOFnI-o49PLQHU2tyqaY2_qpY_h0J-0ka2oWJMgaqgs_93Qp-h_yhZFHw0MZvpdm-b06qa0eMAphaE4ie3YadZD6otTgtJQsBroroAHuwNYQ3UXsSIxkboDUBf0ZbwQYRylDAlJ6OsWQdMH_aKCRY1svYqkxDSuCFuBwBJ0ITJEURRr_wHSYfIBbeyEHJ2byoN401K6fzxgoKbe6LUxH4kuTk02vLPQDJVfQwYaFVtrynRslt3TwVLtzSDyKwtdTpGAsDPV4hv6Co4a89Ss_fX/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
<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.
