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
*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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 http://www.partners.org/complianceline . 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.