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Hello Freesurfers,
I am using mri_glmfit-sim to find significant clusters using permutation simulation. My command is as follows:
mri_glmfit-sim \ --glmdir lh.cn_ad.glmdir \ --perm 1000 3.0 pos \ --cwp 0.05 \ --2spaces \ --bg 1
When I opened the *.sig.masked.mgh, I noticed that some vertices below the cluster forming threshold (3.0) were also included (the lowest value I found in the cluster was around 2.5). These vertices also seem to be on the edge of the cluster. Based on the FsTutorial, the permutation simulation should exclude all vertices below the cluster forming threshold. Is there any sort of smoothing done on the clusters that could have caused the vertices below CFT to be included?
I checked the mail archive and found this thread that have exactly the same question, but with no answer: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html
Thank you, Fengdan
The reason is that you specified a sign (pos). By default, all the FreeSurfer p-values are unsigned. When you specify a sign to mri_glmfit-sim, the unsigned p-value will be converted to a (more significant) signed p-value before applying the CFT. When you look at the unsigned sig map, try setting the visualization threshold to CFT-log10(0.5) and see if you get a perfect match.
On 6/4/2020 2:15 PM, Fengdan Ye wrote:
External Email - Use Caution
Hello Freesurfers,
I am using mri_glmfit-sim to find significant clusters using permutation simulation. My command is as follows:
mri_glmfit-sim \ --glmdir lh.cn_ad.glmdir \ --perm 1000 3.0 pos \ --cwp 0.05 \ --2spaces \ --bg 1
When I opened the *.sig.masked.mgh, I noticed that some vertices below the cluster forming threshold (3.0) were also included (the lowest value I found in the cluster was around 2.5). These vertices also seem to be on the edge of the cluster. Based on the FsTutorial, the permutation simulation should exclude all vertices below the cluster forming threshold. Is there any sort of smoothing done on the clusters that could have caused the vertices below CFT to be included?
I checked the mail archive and found this thread that have exactly the same question, but with no answer: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html
Thank you, Fengdan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I just checked and 3.0+log10(0.5) gives me 2.69, which is exactly the lowest value I saw in *.sig.masked.mgh. Thanks for the explanation!
Best, Fengdan
On Jun 5, 2020, at 1:07 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
The reason is that you specified a sign (pos). By default, all the FreeSurfer p-values are unsigned. When you specify a sign to mri_glmfit-sim, the unsigned p-value will be converted to a (more significant) signed p-value before applying the CFT. When you look at the unsigned sig map, try setting the visualization threshold to CFT-log10(0.5) and see if you get a perfect match.
On 6/4/2020 2:15 PM, Fengdan Ye wrote:
External Email - Use CautionHello Freesurfers,
I am using mri_glmfit-sim to find significant clusters using permutation simulation. My command is as follows:
mri_glmfit-sim \ --glmdir lh.cn_ad.glmdir \ --perm 1000 3.0 pos \ --cwp 0.05 \ --2spaces \ --bg 1
When I opened the *.sig.masked.mgh, I noticed that some vertices below the cluster forming threshold (3.0) were also included (the lowest value I found in the cluster was around 2.5). These vertices also seem to be on the edge of the cluster. Based on the FsTutorial, the permutation simulation should exclude all vertices below the cluster forming threshold. Is there any sort of smoothing done on the clusters that could have caused the vertices below CFT to be included?
I checked the mail archive and found this thread that have exactly the same question, but with no answer: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html
Thank you, Fengdan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Fengdan Ye