Hello, thank you for the reply.
Since posting my question I have written the script below. When I add pixel sizes as suggested, as such
vol_slicer $outputfrom overlay -x 0.35 "12 16 20..." -y 0.35 "10 14.." -z 0.35 "10 14..." -trans -s 2 -out file.png
This gives an "error integer 0.3512 not expected" (or something like that)
Prior to putting the pixel width in, the program would run and creat .png files that look okay, but really not so okay because of the evenly distributed quantity of "activation" outside of the brain. Which is weird because the ICA maps look fine. The images are all the same dimension, and the standard I am using is the one from one of the subjets reg_standard folder created by Melodic, so am pretty sure is sampled to the same space.
Any ideas? Shreads of hope?
Appreciatively,
Varina
#!/bin/bash
for s in $(cat /mnt/hgfs/melodicdesk/FSL-Output/GrotFileLists/p-tstat1);do
standard="/mnt/hgfs/melodicdesk/FSL-Output/5-14DenoisedMO/reg_standard/standard.nii"
directory="/mnt/hgfs/melodicdesk/FSL-Output/5-14DenoisedMO"
stat1="$directory/grot/${s}"
output="$directory/Renderstat/${s}"
cmd="overlay 0 1 $standard -A $stat1 0.95 1 $output"
echo "debug-overlay-cmd=[$cmd]"
$cmd #execute overlay command
overlay 0 1 $standard -A $stat1 0.95 1 $stat2 0.95 1 $output
vol_slicer $output -x "12 16 20 24 28 32 36 40 44 48 52 56 60 64 68 72 76 80 84" -y "10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 78 82 86 90 94 100" -z "10 14 18 22 26 30 34 38 42 46 50 54 58 62 66 70 74 78 82" -trans -s 2 -out $directory/Renderstat/p-test/${s}.png
rename 's/\.png$/\.nii/' *.png
done
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