Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[Fischl, Bruce]

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 
 On Behalf Of Douglas N. Greve
Sent: Friday, October 30, 2020 11:39 AM
To: 李梦君 ; Freesurfer support list 

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" 
发送时间:2020-10-28 05:08:03 (星期三)
收件人: 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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Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[Douglas N. Greve]

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" 
*发送时间:*2020-10-28 05:08:03 (星期三)
*收件人:* 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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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[李梦君]

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" 
发送时间:2020-10-28 05:08:03 (星期三)
收件人: 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


___
Freesurfer mailing list
freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[Douglas N. Greve]

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[李梦君]

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___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer