The segmentation nets typically output one-hot encoded values. So if you have
30 labels, the output layer has 30 outputs, which can be loosely interpreted as
p-values for each label (they will add to 1). To turn it into a segmentation
you take the argmax over the 30-label dimension and toss the underlying
probabilities
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Friday, October 30, 2020 11:39 AM
To: 李梦君 <meng...@csu.edu.cn>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned
into No Statistic Difference after Mapping onto the Subjects
sorry, I don't understand your question. can you elaborate?
On 10/28/2020 11:57 PM, 李梦君 wrote:
External Email - Use Caution
Thanks for your help! I finished the -qcache for every subject before group
analysis with Qdec/mri_label2label. I want to do the correlation analysis
between the significant cortex area and the behavior score. Should I compare
the group analysis without the -qcache before Qdec/mri_label2label?
-----原始邮件-----
发件人:"Douglas N. Greve" <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
发送时间:2020-10-28 05:08:03 (星期三)
收件人: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
抄送:
主题: Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into
No Statistic Difference after Mapping onto the Subjects
When you run your original analysis, you probably smoothed the map before doing
the group analysis. This smoothing would not be in your ROI analysis, and the
difference could be pretty big if the label is small. Also, the area map will
have a jacobian correction that will not be in the raw data.
On 10/19/2020 11:29 PM, 李梦君 wrote:
External Email - Use Caution
Dear FreeSurfer Developers:
I compared the 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, I defined the statistic difference region 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 area value of the label in every single subjects was
extracted, and I found that there is no statistic difference in the area value
between the mild traumatic brain injury patients and health control. I have
checked the segmentation of every subjects and it was a good job done by
FreeSurFer.
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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