Thanks for your advice,

After I got 'out.mgz',  I know for aparc.annot, pysurfer use tksurfer to visualize the map, but for aseg.annot, because it is volume_based analysis, I want to have some thing like this, which has been down in freeview to display the segmentation output of  recon-alll output:



But the different colors for the subcortical regions will be the correspondent z-value for two groups, so what do you think if we can make it by tksurfer, tkmedit or freeview?? 
Thanks very much
De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Douglas N Greve <greve@nmr.mgh.harvard.edu>
Envoyé : mardi 6 décembre 2016 23:21
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation
 
That is a little easier. In matlab you can

seg = MRIread('youseg.mgz');

out = seg;

out.vol = zeros(size(out.vol));

ind = find(seg.vol == segno);

out.vol(ind) = valueforsegno;

MRIwrite(out,'out.mgz');



On 12/06/2016 05:04 PM, Hao wen wrote:
>
>
> Hello, I checked your script, I think this is to map the aparc.annot,
> I have already done that, what I want is to map the aseg.annot
> subcortical segmentation like what we can do for aparc, so do you have
> any idea??
> Thanks in advance
>
> ------------------------------------------------------------------------
> *De :* Hao wen
> *Envoyé :* mardi 6 décembre 2016 18:18
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* RE: [Freesurfer] Volumetric Group Analysis: asegstats2tbale
> result to plot a z-score map for the segmentation
>
> Thanks very much, I will try to look at that:)
>
> Perfect FS,hahah
>
>
>
> ------------------------------------------------------------------------
> *De :* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Douglas Greve
> <greve@nmr.mgh.harvard.edu>
> *Envoyé :* mardi 6 décembre 2016 17:51
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale
> result to plot a z-score map for the segmentation
>
> This is a tricky thing to do. I've created a matlab file to help,
> which you can get from here:
>
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
>
>
> Look at the help for an example on how to use it. You will have to
> specify the list of ROI names and the corresponding list of values
> that you want each ROI to be filled with. See the example
>
>
>
> On 12/6/16 9:57 AM, Hao wen wrote:
>>
>> Hello, FS experts:
>>
>> I have a question for visualizing statistical analysis
>> asegstats2tbale result into a map like what we have done in qdec,
>> which uses the thickness information, so if i want to use the volume
>> information of the different segmentation volume, and after doing
>> z-score for two groups, how can I visualize it into a z map???
>>
>> For example, for the volumetric group analysis, I compute the
>> z-scores for the different subcortical volumes between these two
>> group, how do i visualize the result in sphere???
>>
>>
>> Really need your help
>>
>> Any help will be appreciated
>>
>> Hao
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
>
>
> _______________________________________________
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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--
Douglas N. Greve, Ph.D.
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