External Email - Use Caution
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
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:
External Email - Use Caution
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
External Email - Use Caution
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:External Email - Use CautionDear 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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:
External Email - Use Caution
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:
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1P-25WtOnY2Wauk0IRqjQ_Glo9MoJitYrbEAVRjjODolDbF...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try --slabel fsaverage lh /path/to/lh.areapial.label
On 11/2/2020 10:24 PM, 李梦君 wrote:
External Email - Use Caution
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:External Email - Use Caution 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:External Email - Use CautionDear 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14TWEBeDkPXjXeilF55gARWf14LZXL31wpBSVsRAtFrrf6K...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14TWEBeDkPXjXeilF55gARWf14LZXL31wpBSVsRAtFrrf6K...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
External Email - Use Caution
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:External Email - Use Caution 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:External Email - Use Caution 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:External Email - Use CautionDear 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
External Email - Use Caution
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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No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- *发件人:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> *发送时间:*2020-11-11 23:58:20 (星期三) *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} {Disarmed} Sorry, try this mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:External Email - Use Caution I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volumemri_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:External Email - Use Caution 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:External Email - Use Caution 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:External Email - Use CautionDear 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --seg qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --seg qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
External Email - Use Caution
Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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:
External Email - Use Caution
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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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
External Email - Use Caution
Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
External Email - Use Caution
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:
External Email - Use Caution
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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sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- *发件人:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> *发送时间:*2020-11-12 22:23:13 (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} {Disarmed} {Disarmed} No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0 On 11/12/2020 5:39 AM, 李梦君 wrote:External Email - Use Caution Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command (1) Does the lh_areapial.avgwf.dat contain areas value for all my subject? (2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct? ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005 Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file) -----原始邮件----- *发件人:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> *发送时间:*2020-11-11 23:58:20 (星期三) *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} {Disarmed} Sorry, try this mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:External Email - Use Caution I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volumemri_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:External Email - Use Caution 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:External Email - Use Caution 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:External Email - Use Caution> 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-13 23:03:50 (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 {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
External Email - Use Caution
Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
External Email - Use Caution
Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
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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:
External Email - Use Caution
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:
External Email - Use Caution
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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The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average.
On 11/14/2020 5:24 AM, 李梦君 wrote:
External Email - Use Caution
I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- *发件人:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> *发送时间:*2020-11-13 23:03:50 (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 {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} sorry, I don't know what you are asking On 11/12/2020 8:30 PM, 李梦君 wrote:External Email - Use Caution Thanks! I get only one area value in the lh_areapial.sum file with this command: mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0 (1)Should I extract the area and volume one by one with the following command for each subject: mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0 -----原始邮件----- *发件人:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> *发送时间:*2020-11-12 22:23:13 (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} {Disarmed} {Disarmed} No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0 On 11/12/2020 5:39 AM, 李梦君 wrote:External Email - Use Caution Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command (1) Does the lh_areapial.avgwf.dat contain areas value for all my subject? (2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct? ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005 Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file) -----原始邮件----- *发件人:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU> *发送时间:*2020-11-11 23:58:20 (星期三) *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} {Disarmed} Sorry, try this mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:External Email - Use Caution I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volumemri_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:External Email - Use Caution 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:External Email - Use Caution 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:> > External Email - Use Caution > >> 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > *MailScanner has detected a possible > fraud attempt from > "secure-web.cisco.com" claiming to be* > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple control. Did this correct?
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-16 23:48:37 (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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average.
On 11/14/2020 5:24 AM, 李梦君 wrote:
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I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-13 23:03:50 (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 {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
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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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You mean that you are getting a different result between the voxel wise analysis and the ROI-wise analysis? And you created the ROI from the region that is significant in the voxel-wise analysis? If so, then I think something is wrong
On 11/17/2020 8:08 PM, 李梦君 wrote:
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I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple control. Did this correct?
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-16 23:48:37 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average.
On 11/14/2020 5:24 AM, 李梦君 wrote:
External Email - Use Caution
I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-13 23:03:50 (星期五) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
External Email - Use Caution
Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (星期四) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
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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.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-05 22:37:07 (星期四) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:dgreve@mgh.harvard.edu 发送时间:2020-11-02 23:36:14 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-10-30 23:40:30 (星期五) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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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Yes, what should I do if there is something wrong
-----原始邮件----- 发件人:"Greve, Douglas N.,Ph.D." DGREVE@MGH.HARVARD.EDU 发送时间:2020-11-30 01:22:22 (星期一) 收件人: "freesurfer@nmr.mgh.harvard.edu" 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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
You mean that you are getting a different result between the voxel wise analysis and the ROI-wise analysis? And you created the ROI from the region that is significant in the voxel-wise analysis? If so, then I think something is wrong
On 11/17/2020 8:08 PM, 李梦君 wrote:
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I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple control. Did this correct?
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-16 23:48:37 (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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average.
On 11/14/2020 5:24 AM, 李梦君 wrote:
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I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-13 23:03:50 (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 {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
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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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What are you using to compute the significance of the difference using the ROI average?
On 11/30/2020 7:59 PM, 李梦君 wrote:
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Yes, what should I do if there is something wrong
-----原始邮件----- 发件人:"Greve, Douglas N.,Ph.D." DGREVE@MGH.HARVARD.EDUmailto:DGREVE@MGH.HARVARD.EDU 发送时间:2020-11-30 01:22:22 (星期一) 收件人: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
You mean that you are getting a different result between the voxel wise analysis and the ROI-wise analysis? And you created the ROI from the region that is significant in the voxel-wise analysis? If so, then I think something is wrong
On 11/17/2020 8:08 PM, 李梦君 wrote:
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I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple control. Did this correct?
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-16 23:48:37 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average.
On 11/14/2020 5:24 AM, 李梦君 wrote:
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I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-13 23:03:50 (星期五) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (星期四) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
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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.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-05 22:37:07 (星期四) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:dgreve@mgh.harvard.edu 发送时间:2020-11-02 23:36:14 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-10-30 23:40:30 (星期五) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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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I extracted the value of the ROI average in each subject in the standard space and imported into the SPSS 26.0 to compute the significance of the difference.
-----原始邮件----- 发件人:"Greve, Douglas N.,Ph.D." DGREVE@MGH.HARVARD.EDU 发送时间:2020-12-02 23:31:26 (星期三) 收件人: "freesurfer@nmr.mgh.harvard.edu" 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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
What are you using to compute the significance of the difference using the ROI average?
On 11/30/2020 7:59 PM, 李梦君 wrote:
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Yes, what should I do if there is something wrong
-----原始邮件----- 发件人:"Greve, Douglas N.,Ph.D." DGREVE@MGH.HARVARD.EDU 发送时间:2020-11-30 01:22:22 (星期一) 收件人: "freesurfer@nmr.mgh.harvard.edu" 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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
You mean that you are getting a different result between the voxel wise analysis and the ROI-wise analysis? And you created the ROI from the region that is significant in the voxel-wise analysis? If so, then I think something is wrong
On 11/17/2020 8:08 PM, 李梦君 wrote:
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I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple control. Did this correct?
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-16 23:48:37 (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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average.
On 11/14/2020 5:24 AM, 李梦君 wrote:
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I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-13 23:03:50 (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 {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
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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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I've seen a lot of emails of this sort. Please try running it in matlab y = load('yourroifile.txt') X = load('glmdir/Xg.dat'); [beta rvar] = fast_glmfit(y,X); C = load('glmdir/contrast/C.dat'); [F p] = fast_fratio(beta,X,rvar,C);
You'll have to include the matlab and fsfast/toolbox folders from FREESURFER_HOME in your matlab path
On 12/2/2020 8:11 PM, 李梦君 wrote:
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I extracted the value of the ROI average in each subject in the standard space and imported into the SPSS 26.0 to compute the significance of the difference.
-----原始邮件----- 发件人:"Greve, Douglas N.,Ph.D." DGREVE@MGH.HARVARD.EDUmailto:DGREVE@MGH.HARVARD.EDU 发送时间:2020-12-02 23:31:26 (星期三) 收件人: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
What are you using to compute the significance of the difference using the ROI average?
On 11/30/2020 7:59 PM, 李梦君 wrote:
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Yes, what should I do if there is something wrong
-----原始邮件----- 发件人:"Greve, Douglas N.,Ph.D." DGREVE@MGH.HARVARD.EDUmailto:DGREVE@MGH.HARVARD.EDU 发送时间:2020-11-30 01:22:22 (星期一) 收件人: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
You mean that you are getting a different result between the voxel wise analysis and the ROI-wise analysis? And you created the ROI from the region that is significant in the voxel-wise analysis? If so, then I think something is wrong
On 11/17/2020 8:08 PM, 李梦君 wrote:
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I got the sum area and average area of the label, there is no significant difference between the mTBI group and health control, either.However, the label was significant different in the fsaverage between mTBI group and health control after multiple control. Did this correct?
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-16 23:48:37 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed} {Disarmed}
The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average.
On 11/14/2020 5:24 AM, 李梦君 wrote:
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I am sorry for that my presentation was not that good, the lh_areapial.sum and
lh_areapial.avgwf.dat file are uploaded, I get only one area value in the lh_areapial.sum file
with the following command.
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
My question was that how can I get the value of the area and volume in the standard space for every TBI and health control subjects.
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-13 23:03:50 (星期五) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed} {Disarmed}
sorry, I don't know what you are asking
On 11/12/2020 8:30 PM, 李梦君 wrote:
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Thanks! I get only one area value in the lh_areapial.sum file with this command:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
(1)Should I extract the area and volume one by one with the following command for each subject:
mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped to every subject from the fsaverage) --avgwf lh_areapial.avgwf.dat --accumulate --sum lh_areapial.sum --exclude 0
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-12 22:23:13 (星期四) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed} {Disarmed}
No, the area will be under the "Mean" column. Sorry, I know it is confusing. Also, you will just want to use the 2nd row. You can eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, 李梦君 wrote:
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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2（Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885 2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes mri_segstats --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec) --slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction) --avgwf lh_volume.avgwf.dat (output file) --accumulate --sum lh_volume.sum (output file)
-----原始邮件----- 发件人:"Douglas N. Greve" dgreve@MGH.HARVARD.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-11 23:58:20 (星期三) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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} {Disarmed}
Sorry, try this
mri_segstats --i 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) On 11/5/2020 10:26 PM, 李梦君 wrote:
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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.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-11-05 22:37:07 (星期四) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:dgreve@mgh.harvard.edu 发送时间:2020-11-02 23:36:14 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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.EDUmailto:dgreve@MGH.HARVARD.EDU 发送时间:2020-10-30 23:40:30 (星期五) 收件人: freesurfer@nmr.mgh.harvard.edumailto: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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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/10BOIyrqd9toiQM4yp1HnlJOXJSnaIadOBHos3m5yxuS5xudDsGiVJOg49CqbboMdgBJiFtDmbgkHZB1J1OP0f8Lo1T8GqmNVHlG-y0YCVaRhRaF-5dy58MBYAQPJkwjqaCQadne2-ro834ulwG-hue1dLDdPjumYMraaUUS5Yp1uWgQbYKSUQGJe-Hp4UGjJrHGpej7bVQjJ2efMTa-GiJ3tUXHVU3MwtvJ2MzdBPtdYe2Ads_743QHUTtMYeNRuzlKTMIy8U25p9BL-npQGKg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1lUr_QYPnjU6ixlJELmYr0ZPPQC7ad5-DFNXxMk7PjTSQ9g0tzjLH8z02NNO_eLj0nhvjhzqdwj9bpGlJwD3UsyJQyg3xwLeCnbXQPCEIA-noyDkDhaH--0-w5eK3e3ozNYIzMznH6U948gsMJWSwMSf0WTp_v0rnRB1fAcdip87a_biPDfFiDIjibDOO8GbLnFZUPHwXnBaSvF7jBrL8lZDcTw7trDO73RodaRpc7AOKKzwzhiwUjavrw4V2q15lxqLFTI2bZKfxjpqH3nLldQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1Ie_V5kKn938r8IRThuaFloiaCI81Q0H0oWXcNyvc1JaA4YMwk2oU0QyoFaKYhF29vZDjDOc2EbdCGBU5Ae3PqkdcIVav-l__UauXqCsilEzQvT_zLUnqfP6wEBq9idW0oLVE0Iavnu-IApFzHCy5-qQcrn5Yg2ynbO7w-aON1HwbuFFKkaVkL1LerJ179cNagxY_fiFzFqityYi4zbDxg_TTId4tSzFbF7hXvbmasJCz3mMyh1l5hPvWwc74DOgwPT7929stAfAgvYH3UHSknA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1_oVCjq-oTdUFIpyfvgqsWLwxG97UsbbIJecPE-DeUzCBCutW0l4lZiU4jeV1q4OecUhTp8TzzTXVBBQvyCzxTUnneB2j2W9y3GdrQBTP_3NP-AILNxneTrQqS6GkjsoxvQoxVw610ztuveBKpsr1OSe1QFic_17P2-kFQf2h-5iEO5Hvu2YIwBRXhpJp1_0Q2csU5GX_56tksFW0-o_iRjxhFcpAeIuiBB9wQDLdEUWLeeE1eIdAFiwH_5OZfP7ovpI_9RPAtGOhzzgY2TktOg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Greve, Douglas N.,Ph.D.
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李梦君