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I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volume
mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-05 22:37:07 (星期四) 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 {Disarmed} {Disarmed}
Try --slabel fsaverage lh /path/to/lh.areapial.label
On 11/2/2020 10:24 PM, 李梦君 wrote:
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Thank you very much! I tried to extract the areas with the following codes: mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel lh.areapial.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_areapial.avgwf.dat (output file) --accumulate --sum lh_areapial.sum (output file) I did not get a text file including the areas of all subjects. Is this code correct？
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@mgh.harvard.edu 发送时间:2020-11-02 23:36:14 (星期一) 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 {Disarmed}
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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