mri_surfcluster statistics and label question

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Yang, Daniel

9 Nov 2015 9 Nov '15

10:51 a.m.

Dear FreeSurfer experts,

In the output mri_surfcluster (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSum...), what is the statistics behind the Max?

Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two lines of contrast), but not Z-statistics?

Also, I notice that the annotation is picking only one of the anatomical regions in which the cluster is located. Is it possible to tell all the anatomical regions that a label has?

Thanks, Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu

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Douglas N Greve

9 Nov 9 Nov

6:02 p.m.

On 11/09/2015 10:51 AM, Yang, Daniel wrote:

...

Dear FreeSurfer experts,

In the output mri_surfcluster (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSum...), what is the statistics behind the Max?

Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two lines of contrast), but not Z-statistics?

it is the maximum of the abs(-log10(p))

...

Also, I notice that the annotation is picking only one of the anatomical regions in which the cluster is located. Is it possible to tell all the anatomical regions that a label has?

No, not from that output.

...

Thanks, Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Yang, Daniel

6:46 p.m.

Hi Doug,

Got it! Sorry that I keep forgetting this. So it’s an exponent statistic.

The reviewers asked for a statistic and df. I think I can convert it to a Z-statistic so it’s more “conventional”.

I also noticed that qdec provides a df when I set up the model. It is valid to use that df to derive the t-statistic?

Best, Daniel

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu On 11/9/15, 6:02 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote: > > >On 11/09/2015 10:51 AM, Yang, Daniel wrote: >> Dear FreeSurfer experts, >> >> In the output mri_surfcluster (e.g., >> >>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisCluster >>Summary), >> what is the statistics behind the Max? >> >> Is it either t-statistic (if only 1 line of contrast) or F-statistic >> (if two lines of contrast), but not Z-statistics? >it is the maximum of the abs(-log10(p))

Douglas Greve

10:57 p.m.

There should be a t.mgh file there (or maybe F.mgh). You can just pull the value out of the vertex out of that.

On 11/9/15 6:46 PM, Yang, Daniel wrote:

...

Hi Doug,

Got it! Sorry that I keep forgetting this. So it’s an exponent statistic.

The reviewers asked for a statistic and df. I think I can convert it to a Z-statistic so it’s more “conventional”.

I also noticed that qdec provides a df when I set up the model. It is valid to use that df to derive the t-statistic?

Best, Daniel

Yang, Daniel

10 Nov 10 Nov

6:26 a.m.

Thanks! The F.mgh works well, and it also increases precision as converting from the exponent itself is less precise.

-- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang@yale.edu On 11/9/15, 10:57 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote: >There should be a t.mgh file there (or maybe F.mgh). You can just pull >the value out of the vertex out of that. > >On 11/9/15 6:46 PM, Yang, Daniel wrote: >> Hi Doug, >> >> Got it! Sorry that I keep forgetting this. So it’s an exponent >>statistic. >> >> The reviewers asked for a statistic and df. I think I can convert it to >>a >> Z-statistic so it’s more “conventional”. >> >> I also noticed that qdec provides a df when I set up the model. It is >> valid to use that df to derive the t-statistic? >> >> Best, >> Daniel >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl >ianceline&d=AwIGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MORXy6GkKdTAw3V58rxz >UZGOKpGXPDgqUHY&m=0RrRr1_vfqKidnHFsGCektDHjSDuECMNGanFYSOjE8w&s=Go4hBLGpzA >KSdkn0TGgNfAvJpyToUgrusCYlC8IFuAY&e= . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail.

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Douglas Greve
Douglas N Greve
Yang, Daniel