The FA values are used to compute a p-value at each voxel. The p-value map is thresholded using the threshold you supply (3 in this case). Clusters are formed based on the number neighboring/contiguous voxels above threshold. The p-value for the cluster is determined based on the number of voxels in the cluster, the threshold you used, the amount of smoothing, and the number of voxels in the brain mask (ie, the search space). doug

Antonella Kis wrote:

I understand that but how this value is related to my FA values? Is p accounting for the FA's intensity within a cluster?

THANKS! Antonella

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*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, January 26, 2012 11:30 AM *Subject:* Re: [Freesurfer] cwp threshold

This is the maximum p-value for a cluster that will be reported. You can also raise the p-value to report more clusters, but you probably cannot get anything published with p>.05

Antonella Kis wrote:

...

Dear all,

I would like to know if while doing a group analysis for my FA data and I do the correction by multiple comparisons for the clusters:

mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --grf 3 neg \ --cwpvalthresh .05 \ --overwrite

what exactly is defined the cwpvalthresh. I mean I know that this is a cluster-wise p-value threshold but is this calculated from or based on the FA intensity values?

Thank you very much for your clarification. Antonella

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