3dClustSim

3dClustSim for determining cluster size: 3dClustSim -mask NN.nii -fwhmxyz 12.2383 12.119 10.4415 -pthr .001 -athr .1 .05 .01 -iter 10000 -nodec -NN 2 -prefix cluster_size_needed

the mask file is the a mask of the voxels you are going to test for significance in your data the fwhmxyz is the smoothness of your data as determined by SPM (SPM.xVol.FWHM), FSL (smoothest), AFNI (3dfwhmx), FAST (fmri_fwhm). [Note: if you are using FSL, you need to convert the smoothness to mm] the pthr is a list of the voxelwise p-values to use the athr is a list of the cluster thresholds to use the iter is the number of iterations to use. I wouldn't use anything below 5000. the nodec just rounds the number of voxels needed in a cluster up to the nearest whole number the NN option specifies the neighbor (1=face-connected, 2=edge connected, 3=corner connected). the prefix option is the prefix of the output. the output file is a textfile named prefix.NN?.1D