Hi AFNI experts,
Is there any way in AFNI/SUMA to visualize only the edges of ROIs, without filling inside each ROI?
Thanks in advance,
Soo Hyun
Hi AFNI experts,
Is there any way in AFNI/SUMA to visualize only the edges of ROIs, without filling inside each ROI?
Thanks in advance,
Soo Hyun
Hi Soo Hyun,
Here’s a short script where almost all the action happens in just two steps. If you are careful, you can actually do this mostly in a single 3dcalc command using relative indexing, but I think this is a little clearer and more flexible.
#!/bin/tcsh
set dset = $1
set prefix = “edgy_rois”
3dLocalstat -stat stdev -nbhd ‘SPHERE(-1.42)’ -prefix temp_sd.nii.gz -overwrite
$dset
#3dLocalstat -stat stdev -nbhd ‘RECT(-1,-1,-1)’ -prefix temp_sd.nii.gz -overwrite \
3dcalc -a $dset -b temp_sd.nii.gz -prefix $prefix.nii.gz -overwrite
-expr ‘a*step(b)’
3drefit -cmap INT_CMAP $prefix.nii.gz
Another tricky way to show edges is to make surfaces of all the regions and then use suma to draw the surface nodes in the afni GUI.
mkdir surfs
cd surfs
IsoSurface -isorois+dsets -input …/myrois.nii -o mysurfs.gii
Then start afni in the volumetric data directory and suma with the surfaces you just created.
afni -niml …/
suma -onestate -i *.gii -sv …/myrois.nii
In AFNI, set the underlay to some desired dataset. In suma, press ‘t’ for suma to talk to afni, and the surface edges will appear in the afni viewer. You can control the thickness of the edge lines with the Control Surfaces menu in afni.
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