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Dear FreeSurfer experts:

I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'.

Now,I have known that cortical thickness in this file is in standard space.But I don't understand why it is an average of 40 subjects.

Is it not CT measures an individual in standard space?

I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices.

Is there any way I can get individual ROI in standard space if I want to compute mean CT measures of each ROI?

or Can I use file '$SUBJECTS_DIR/fsaverage/label/?.annot' as atlas directly?

-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@mgh.harvard.edu 发送时间:2021-10-09 10:36:07 (星期六) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] Question about fsaverage

On 10/8/2021 8:51 PM, Dongyue Zhou wrote:

External Email - Use Caution

Dear FreeSurfer experts:

I want to know cortical thickness in this file 'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard space or in native space.

standard

Is not the common coordinate system the same as standard space?

yes, they are the same

And if mean ROI CT measures computed by this file is the same as that computed by file 'subjectname/stats/?h.thickness'.

They are not the same. One is an average of 40 subjects, the other is an individual.

If not,I want to use fsaverage file to compute mean CT measures of each ROI,how should I locate each region?

I don't know what you mean

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The file contains the cortical thickness for a single subject, mapped to standard space.

Why do you think it was for 40 subjects? Could it be that this is a confusion, because the *fsaverage template subject* was created from that many subjects?

Best,

Tim

On 10/10/2021 3:44 PM Dongyue Zhou zhoudongyue@mail.dlut.edu.cn wrote:

External Email - Use Caution

Dear FreeSurfer experts:

I use the 'qcache' command to get the file '$SUBJECTS_DIR/subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh'.

Now,I have known that cortical thickness in this file is in standard space.But I don't understand why it is an average of 40 subjects.

Is it not CT measures an individual in standard space?

I can get cortical thickness in each vertice by reading this file in matlab. And I know mean CT is computed by dividing sum CT of all ROI vertices by the number of ROI vertices.

Is there any way I can get individual ROI in standard space if I want to compute mean CT measures of each ROI?

or Can I use file '$SUBJECTS_DIR/fsaverage/label/?.annot' as atlas directly?

-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@mgh.harvard.edu 发送时间:2021-10-09 10:36:07 (星期六) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] Question about fsaverage

On 10/8/2021 8:51 PM, Dongyue Zhou wrote:

    External Email - Use Caution        

Dear FreeSurfer experts:

I want to know cortical thickness in this file 'subjectname/surf/?h.thickness.fwhm10.fsaverage.mgh' is in standard space or in native space.

standard

Is not the common coordinate system the same as standard space?

yes, they are the same

And if mean ROI CT measures computed by this file is the same as that computed by file 'subjectname/stats/?h.thickness'.

They are not the same. One is an average of 40 subjects, the other is an individual.

If not,I want to use fsaverage file to compute mean CT measures of each ROI,how should I locate each region?

I don't know what you mean

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany