Iterating through folders for specific files in BASH - bash

Question

I'm new to coding and am trying to iterate through folders to find a specific file (called the same thing in each folder). I have 3 folders (CONTROL, GROUP1, and GROUP2). Each folder has 2 subfolders in it from the folder names (2 3 4 5 6 7. Each subfolder has a file in it with the subfolder name such as 2_diff.nii or 3_diff.nii. I'd like the code to go into each folder, find the subfolders, and then perform an analysis of the file in there. The problem is that my code seems to be looking for each subfolder in each main folder and each main folder only has 2 of the subfolders out of (2 3 4 5 6 7). Any tips would be greatly appreciated - thank you!!
Folders=(CONTROL GROUP1 GROUP2)
SubFolders=(2 3 4 5 6 7)
data_source=/Users/sheena/Desktop/test/
for j in ${Folders[#]}; do
cd ${data_source}/${j}/
for i in ${SubFolders[#]}; do
fslroi ${i}_diff.nii ${i}_nodif 0 1 #I want to analyze the file <subfolder>_diff.nii and name the output as <subfolder>_nodif.nii
done
done

Answer 1

The way I understand your question is that in each of the directories CONTROL, GROUP1, and GROUP1 there are 2 files of the form x_diff.nii where x is a digit between 2 and 7. At least that's how I read your code.
You don't in advance know which two digits there are.
The easiest way I see it is to run through all possible SubFolders like you do, but use the continue statement early to jump to the next if it doesn't exist:
Folders=(CONTROL GROUP1 GROUP2)
SubFolders=(2 3 4 5 6 7)
data_source=/Users/sheena/Desktop/test/
for j in ${Folders[#]}; do
cd ${data_source}/${j}/
for i in ${SubFolders[#]}; do
if [[ ! -e ${i}_diff.nii ]]; then
continue
fi
fslroi ${i}_diff.nii ${i}_nodif 0 1
done
done
You could replace the if clause above with a single line:
for i in ${SubFolders[#]}; do
[[ -e ${i}_diff.nii ]] || continue
fslroi ${i}_diff.nii ${i}_nodif 0 1
done
But I find the more expressive if - fi block easier to read and understand, and that's important too.