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...@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 <zhoudong...@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 ?
> >
> >
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