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Dear FreeSurfer experts:
I use the command recon-all qcache to get filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
I want to know mean CT measures of every ROI after registraion in one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices.
Can I use fsaverage/label/?.annot as atlas to calculate mean cortical thickness of every ROI directly?
Or should I transfer sub_01/label/?.annot to fsaverage ?
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You should have a look at the 'aparcstats2table' command that comes with FreeSurfer, it does exactly what you want. There is no need to compute this manually.
https://secure-web.cisco.com/1y8MoV_lySYxRtn11tB5a6H64yS1J9YFCgCSFtxDPRbXFec...
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 10/08/2021 8:28 AM Dongyue Zhou zhoudongyue@mail.dlut.edu.cn wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I use the command recon-all qcache to get filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
I want to know mean CT measures of every ROI after registraion in one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices.
Can I use fsaverage/label/?.annot as atlas to calculate mean cortical thickness of every ROI directly?
Or should I transfer sub_01/label/?.annot to fsaverage ?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1vsRp-aD0Q2p94vqaG6vqN3kh1Um6IDZ_LwLAPFxpdxzzjf...
External Email - Use Caution
Oh sorry, ignore my last mail, I misread your question. aparcstats2table will compute the values for native space, and if I interpret your email correctly, you want them in standard space.
Sorry for the confusion,
Tim
On 10/08/2021 8:28 AM Dongyue Zhou zhoudongyue@mail.dlut.edu.cn wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I use the command recon-all qcache to get filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
I want to know mean CT measures of every ROI after registraion in one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices.
Can I use fsaverage/label/?.annot as atlas to calculate mean cortical thickness of every ROI directly?
Or should I transfer sub_01/label/?.annot to fsaverage ?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1KeWlEN2ywg3XWmiIk51vJenarixEySvruOwlAqz3ANW8se...
External Email - Use Caution
Yes,I want to compute them in standard space.But I don't know which atlas I should use?
-----原始邮件----- 发件人: "Tim Schäfer" ts+ml@rcmd.org 发送时间: 2021-10-08 15:27:32 (星期五) 收件人: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] Confusion about mean CT measures after registration
External Email - Use CautionOh sorry, ignore my last mail, I misread your question. aparcstats2table will compute the values for native space, and if I interpret your email correctly, you want them in standard space.
Sorry for the confusion,
Tim
On 10/08/2021 8:28 AM Dongyue Zhou zhoudongyue@mail.dlut.edu.cn wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I use the command recon-all qcache to get filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
I want to know mean CT measures of every ROI after registraion in one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices.
Can I use fsaverage/label/?.annot as atlas to calculate mean cortical thickness of every ROI directly?
Or should I transfer sub_01/label/?.annot to fsaverage ?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1KeWlEN2ywg3XWmiIk51vJenarixEySvruOwlAqz3ANW8se...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1SUGwhn9Xb15yB6G8_lF5VzGlGThYmkGa9CUUWC5Db0V8LP...
External Email - Use Caution
Yes,I want to compute them in standard space.But I don't know which atlas I should use? > -----原始邮件----- > 发件人: "Tim Schäfer" ts+ml@rcmd.org > 发送时间: 2021-10-08 15:27:32 (星期五) > 收件人: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu > 抄送: > 主题: Re: [Freesurfer] Confusion about mean CT measures after registration > > External Email - Use Caution > > Oh sorry, ignore my last mail, I misread your question. aparcstats2table will compute the values for native space, and if I interpret your email correctly, you want them in standard space. > > Sorry for the confusion, > > Tim > > > On 10/08/2021 8:28 AM Dongyue Zhou zhoudongyue@mail.dlut.edu.cn wrote: > > > > > > External Email - Use Caution > > > > Dear FreeSurfer experts: > > > > I use the command recon-all qcache to get filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file. > > > > I want to know mean CT measures of every ROI after registraion in one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices. > > > > Can I use fsaverage/label/?.annot as atlas to calculate mean cortical thickness of every ROI directly? > > > > Or should I transfer sub_01/label/?.annot to fsaverage ? > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://secure-web.cisco.com/1KeWlEN2ywg3XWmiIk51vJenarixEySvruOwlAqz3ANW8se... > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1W5AoPa8JwbrRW7FK22qRJFVBmTfXKQoE5U1THFZhm_4fFg...
You want to measure cortical thickness in standard space? It is not something we typically do, but I guess you could apply the taliarach registration to the surfaces and recompute the thickenss, eg, mris_apply_reg --lta lh.white ../mri/transforms/talairach.lta lh.white.tal mris_apply_reg --lta lh.pial../mri/transforms/talairach.lta lh.pial.tal mris_place_surface --thickness lh.white.tal lh.pial.tal 20 5 lh.thickness.tal This will generate a thickness map. You can then run mris_anatomical_stats -t lh.thickness.tal -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.tal.stats -b -a ../label/lh.aparc.annot subjectname lh white
On 10/8/2021 9:59 AM, Dongyue Zhou wrote:
External Email - Use Caution
Yes,I want to compute them in standard space.But I don't know which atlas I should use?
-----原始邮件----- 发件人: "Tim Schäfer" ts+ml@rcmd.org 发送时间: 2021-10-08 15:27:32 (星期五) 收件人: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] Confusion about mean CT measures after
registration
External Email - Use Caution
Oh sorry, ignore my last mail, I misread your question.
aparcstats2table will compute the values for native space, and if I interpret your email correctly, you want them in standard space.
Sorry for the confusion,
Tim
On 10/08/2021 8:28 AM Dongyue Zhou zhoudongyue@mail.dlut.edu.cn
wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I use the command recon-all qcache to get
filesub_01/surf/lh.thickness.fwhm10.fsaverage.mgh file.
I want to know mean CT measures of every ROI after registraion in
one subject. And I know mean CT is calculated by dividing CT of all vertices by the number of vertices.
Can I use fsaverage/label/?.annot as atlas to calculate mean
cortical thickness of every ROI directly?
Or should I transfer sub_01/label/?.annot to fsaverage ?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1KeWlEN2ywg3XWmiIk51vJenarixEySvruOwlAqz3ANW8se...
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