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."
<dgr...@mgh.harvard.edu><mailto:dgr...@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.edu><mailto: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?
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发件人:"Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-16 23:48:37 (星期一)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-13 23:03:50 (星期五)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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
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发件人:"Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-12 22:23:13 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-11 23:58:20 (星期三)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-05 22:37:07 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-11-02 23:36:14 (星期一)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-10-30 23:40:30 (星期五)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto: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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