I think the reason for this may be that the data in fsaverage space (after mris_preproc) will have had a jacobian correction which will not be in data on the native surface. For this reason, I would not use #1. #2 is fine.You can apply your label in fsaverage space to the y.mgh used as input to mri_segstats specifying the label using --slabel and using --avgwf output and also use --accumulate; run it with --help for more info. This will create a text file of the areas or volumes (depending upon which y.mgh you input) all your subjects for that label.


On 10/30/2020 10:37 PM, 李梦君 wrote:

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Dear Professors:  
  
  I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found statistic difference region in the cortex area, volume respectively. I defined the statistic difference regions as a label on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview  Then the value of the label in every single subjects was extracted, and I found that there is no statistic difference in the value regarding to the area and volume between the mild traumatic brain injury patients and health control subjects. Following are my questions:

(1)Can I carry out correlation analysis between the cortex area and volume with the behavior scores through these non-statistical extracted values?
 
(2)Can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects, and carry out correlation analysis between the cortex area and volume with the behavior scores. How can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects

Best wishes
Mengjun Li


-----原始邮件-----
发件人:"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
发送时间:2020-10-30 23:40:30 (星期五)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject

Do you mean you compared your TBI subjects against fsaverage? That is not proper methodology.

On 10/29/2020 9:51 PM, 李梦君 wrote:

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Dear FreeSurfer Developers:

   I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area and volume for every subject in the fsaverage with the code of mri_segstats

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra.

Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University

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