I want to creat a ROI based on a cluster in an activation map
To get the mask, I tried to use the following command:
3dmerge -prefix mask_rs-rw -1clip 2.807 -dxyz=1 -1clust_order 1 173 $spath/glts/GLM_glts_rs-rw+tlrc.‘’
######The inputfile “GLM_glts_rs-rw+tlrc.‘’” comes from the result of t-test analysis.
But, when i get the mask_rs-rw file, there are only 9 ROIs. Actually, there are more than 9 active regions in the GLM_glts_rs-rw+tlrc. file. It seems that some regions lost.
is there anything wrong in the script?
Have you tried using 3dClusterize?
I think this would greatly simplify things. You can use this option to get a map of the ROIs (numbered with largest as #1, next largest as #2, etc.) output:
-pref_map PPP :The prefix/filename of the output map of cluster ROIs.
The 'map' shows each cluster as a set of voxels with the
same integer. The clusters are ordered by size, so the
largest cluster is made up of 1s, the next largest of 2s,
(def: no map of clusters output).