Dear Travis,
There might be a direct functionality for this in CAT12 but you can do
it manually in SPM12:
* Save > all clusters (n-ary): clusters_mask.gii
* m = gifti('clusters_mask.gii');
% compute cluster sizes
histc(m.cdata,0:max(m.cdata))
20147 113 47 43 ...
% First value is background
* If I'm interested in the mean beta_1 value within the cluster with 113
vertices, I would do:
g = gifti('beta_0001.gii');
mean(g.cdata(find(m.cdata==1)))
spm_summarise should do this for you automatically but this function
hasn't been updated to handle surface data yet, and it seems that the
option to save a mask of the current cluster does not work as expected
hence relying on n-ary here.
Best regards,
Guillaume.
On 11/04/17 21:39, Travis Beckwith wrote:
> Hi,
>
> I've been using the CAT12 toolbox to generate cortical thickness estimates for analyses. Does anyone know of a way to use a custom mask to extract values from the analysis output files? Specifically, I would like to make a mask from a statistically significant cluster and then use that mask as an ROI for extracting the beta values from the beta_000*.gii files to examine how much confounding variables change the beta values. I understand how to do this for a VBM analysis in SPM when the output are nifti files, but I'm having trouble with the gifti files.
>
> Thanks,
>
> Travis
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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