get mask file in ROI analysis

AFNI Message Board
1

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.‘[1]’
######The inputfile “GLM_glts_rs-rw+tlrc.‘[1]’” 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?

2

Have you tried using 3dClusterize?
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/3dClusterize_sphx.html#ahelp-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,
                 etc.
                 (def:  no map of clusters output).

–pt