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Hello Experts,
I have a question regarding grey matter thickness map and signal to noise ratio. Does smoothing of the map increase signal to noise during surface based cortical thickness analyses? if yes or no, why? This question was asked by a reviewer in one of our manuscript because he/she thinks that one of the reasons to perform smoothing is to comply with random field theory hypotheses, when controlling for multiple testing.
We did apply multiple comparison corrections using monte carlo simulation with cluster threshold of 2, 5000 iterations, and bonferroni.
Thanks alot.
best, Paul
For statistical analysis, the reviewer is right, see https://pubmed.ncbi.nlm.nih.gov/29288131 We are recommending permutation analysis, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0... or https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 9/30/2020 9:23 AM, miracle ozzoude wrote:
External Email - Use Caution
Hello Experts,
I have a question regarding grey matter thickness map and signal to noise ratio. Does smoothing of the map increase signal to noise during surface based cortical thickness analyses? if yes or no, why? This question was asked by a reviewer in one of our manuscript because he/she thinks that one of the reasons to perform smoothing is to comply with random field theory hypotheses, when controlling for multiple testing.
We did apply multiple comparison corrections using monte carlo simulation with cluster threshold of 2, 5000 iterations, and bonferroni.
Thanks alot.
best, Paul
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 Doug. I appreciate it. I guess we will have to redo our analyses based using permutation and hope the results are the same
On Wed, Sep 30, 2020 at 10:22 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
For statistical analysis, the reviewer is right, see https://pubmed.ncbi.nlm.nih.gov/29288131 We are recommending permutation analysis, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0... or https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 9/30/2020 9:23 AM, miracle ozzoude wrote:
External Email - Use CautionHello Experts,
I have a question regarding grey matter thickness map and signal to noise ratio. Does smoothing of the map increase signal to noise during surface based cortical thickness analyses? if yes or no, why? This question was asked by a reviewer in one of our manuscript because he/she thinks that one of the reasons to perform smoothing is to comply with random field theory hypotheses, when controlling for multiple testing.
We did apply multiple comparison corrections using monte carlo simulation with cluster threshold of 2, 5000 iterations, and bonferroni.
Thanks alot.
best, Paul
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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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Hello Doug,
Any advantages of surface-based smoothing of the gm thickness maps beside increasing signal to noise ratio? I read the paper and based on the results and conclusion, mcz with higher threshold and fwhm should be fine (though permutation is recommended) for thickness.
best, paul
On Wed, Sep 30, 2020 at 10:37 AM miracle ozzoude miracooloz@gmail.com wrote:
Thank you very much Doug. I appreciate it. I guess we will have to redo our analyses based using permutation and hope the results are the same
On Wed, Sep 30, 2020 at 10:22 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
For statistical analysis, the reviewer is right, see https://pubmed.ncbi.nlm.nih.gov/29288131 We are recommending permutation analysis, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0... or https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm
On 9/30/2020 9:23 AM, miracle ozzoude wrote:
External Email - Use CautionHello Experts,
I have a question regarding grey matter thickness map and signal to noise ratio. Does smoothing of the map increase signal to noise during surface based cortical thickness analyses? if yes or no, why? This question was asked by a reviewer in one of our manuscript because he/she thinks that one of the reasons to perform smoothing is to comply with random field theory hypotheses, when controlling for multiple testing.
We did apply multiple comparison corrections using monte carlo simulation with cluster threshold of 2, 5000 iterations, and bonferroni.
Thanks alot.
best, Paul
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
Only that the parametric assumptions are better met and so mcz controls the FPR better
On 9/30/2020 2:29 PM, miracle ozzoude wrote:
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Hello Doug,
Any advantages of surface-based smoothing of the gm thickness maps beside increasing signal to noise ratio? I read the paper and based on the results and conclusion, mcz with higher threshold and fwhm should be fine (though permutation is recommended) for thickness.
best, paul
On Wed, Sep 30, 2020 at 10:37 AM miracle ozzoude <miracooloz@gmail.com mailto:miracooloz@gmail.com> wrote:
Thank you very much Doug. I appreciate it. I guess we will have to redo our analyses based using permutation and hope the results are the same On Wed, Sep 30, 2020 at 10:22 AM Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: For statistical analysis, the reviewer is right, see https://pubmed.ncbi.nlm.nih.gov/29288131 We are recommending permutation analysis, see https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm or https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm On 9/30/2020 9:23 AM, miracle ozzoude wrote:External Email - Use Caution Hello Experts, I have a question regarding grey matter thickness map and signal to noise ratio. Does smoothing of the map increase signal to noise during surface based cortical thickness analyses? if yes or no, why? This question was asked by a reviewer in one of our manuscript because he/she thinks that one of the reasons to perform smoothing is to comply with random field theory hypotheses, when controlling for multiple testing. We did apply multiple comparison corrections using monte carlo simulation with cluster threshold of 2, 5000 iterations, and bonferroni. Thanks alot. best, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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