You can run mri_surfcluster with your fdr threshold as the --thmin
value. This will output cluster number (ocn) map. This will assign the
cluster number to a vertex. You can then use mri_segstats with --seg
ocn.mgz --excludeid 0 and input being the mean thickness or area maps.
When you use area as thhe input, make sure to --accumulate to get the
total area. You can get an area map in the same way that you got the
thickness map, ie, mris_preproc, etc

On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote:
>
>         External Email - Use Caution
>
> Dear Greve,
>
> Thank you for your quick respons.
>
> Yes, I believe that is what I mean. Let me illustrate with some
> (fictive) data;
> We were able to prove these data for the entire hemisphere as can be
> seen below.
>
>       
>
>       
>
> *Group 1*
>
>       
>
> *Group 2*
>
>       
>
> *Difference*
>
>       
>
> */Sig./*
>
> Thickness
>
> (in mm)
>
>       
>
> Left
>
>       
>
> 1.48
>
>       
>
> 1.46
>
>       
>
> .004
>
>       
>
> .19
>
> Right
>
>       
>
> 1.46
>
>       
>
> 1.46
>
>       
>
> .003
>
>       
>
> .03
>
>
>
>
>
>
> However, we would like to provide similar data in our vertex-base
> analyses:
>
> *Significantly different clusters between group 1 and group 2*
>
>       
>
> *Cortical thickness group 1*
>
>       
>
> *Cortical thickness group 2*
>
>       
>
> *Difference in mm2*
>
>       
>
> */Sig./*
>
> Left Cuneus
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> 0.013
>
> Left Fusiform gyrus
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> 0.021
>
> Right Paracentral lobule
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> 0.001
>
> Right parahippocampal gyrus
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> ?
>
>       
>
> 0.002
>
>
> Does this clarify my question?
>
> Best wishes,
> Aicha
>
>
>
> ------------------------------------------------------------------------
> *Van:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> namens Greve, Douglas
> N.,Ph.D. <DGREVE@mgh.harvard.edu>
> *Verzonden:* donderdag 31 oktober 2019 16:25
> *Aan:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex
> base level
> I'm not sure what you mean. Do you want the mean thickness of a cluster
> and/or its surface area?
>
> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
> >
> >         External Email - Use Caution
> >
> > Dear developers,
> >
> > For a case-control study we are comparing the cortical thickness and
> > cortical surface area on a vertex-base level, for which we found
> > significant differences throughout the brain.
> >
> > Is it possible that, in addition to the significance values (p < .05
> > after FDR correction) on a vertex-base level, we can include the exact
> > thickness or surface area value (or difference) of the significant
> > clusters on a vertex base-level between the groups. In order words, to
> > provide some measures to highlight the size of the significant cluster
> > or the differences in cortical thickness / cortical surface area to
> > provide clinically useful context. For instance, a command comparable
> > to 'voxel size' in TBSS.
> >
> > As this is my first time using Freesurfer any help that you could
> > offer on this matter would be highly appreciated.
> >
> > Best wishes,
> > Brigitte Dijkshoorn
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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