subdivide atlas region

[rolinskira]

Hi all,

I am using whereami to mask the left/right superior temporal gyrus with the MNI macro labels atlas. Is there a command I could use to sub divide the mask into a anterior, middle, and posterior regions (3 smaller masks)? 3dcalc perhaps? What would be the options for that?

Thank you!!

[dglen]

This can be accomplished a few ways. Here is a short script that subdivides based on distance from a particular coordinate. In this case, I just hand-picked it.

#!/bin/tcsh

subdivide_ROI_by_distance.csh

subdivide a region of interest based on distance from a particular xyz coordinate

set baseset = MNIa_caez_ml_18+tlrc
set coords = ( ‘-15’ ‘-4’ ‘-7’ )
set maskval = 72
set subn = 3

calculate distance map for mask (simple euclidean distance)

3dcalc -a $baseset -expr “equals(a,$maskval)*sqrt(($coords[1]-x)^2 + ($coords[2]-y)^2 + ($coords[3]-z)^2)”
-prefix roi_distmap.nii.gz -overwrite
set maxdist = 3dBrickStat -max roi_distmap.nii.gz

subdivide the regions into thirds, for instance

set minsubroi_dist = 0
foreach subroi (count -digits 1 1 $subn)
set subroi_dist = ccalc -float -expr "$maxdist*$subroi/$subn"
3dcalc -a roi_distmap.nii.gz -b $baseset -expr “equals(b,$maskval)$subroiwithin(a,$minsubroi_dist, $subroi_dist)”
-overwrite -prefix subroi_$subroi.nii.gz
set minsubroi_dist = $subroi_dist
end
3dMean -max -prefix allsubrois.nii.gz -overwrite subroi_*.nii.gz

[rolinskira]

Wow, this was a huge help! Thank you so much!