Dynamically execute functions in different folders using bash - bash

Question

I have two folders: control and patients both with several folders inside, belonging to one individual each.
I want to do two things:
Create inside the folder for each individual a new folder called cortical_maks and inside that one, three more, called accumebens, putamen, caudate
Inside each individual folder, there are images in img format I want to convert to nii.gz using the funtion fslchfiletype.
This is what I have so far:
DIR="/media/Roy"; cd "$DIR/Analysis"
for group in Controls Patients; do
for case in $group/*; do
[ -d $case ] || continue #if its not a folder
mkdir $DIR/Analysis/$case/Cortical_masks && cd $_
mkdir accumbens putamen caudate
for file in $DIR/Analysis/$case/ROIS2/rs_roi/*.img; do
fslchfiletype NIFTI_GZ "$file"
done;
done;
done;
There are two problems with this code.
The second time you run it, the folder cortical masks is created in the main folders, that is controls and patients, that is, outside the folder it´s supposed to work.
Also, it just converts img to niig.gz for one folder at a time. First time you execute the script, converts imgs for the folder belonging to the first individual, etc

Answer 1

Question 01 :
The second time you run it, the folder cortical masks is created in the main folders, that is controls and patients. I want it in a way that doesn´t create new folders if there is already one with the same name.
I suggest you to use an if loop to verify if the folder cortical_mask exist before to run your code :
#check if the folder exist, if yes = true so we add ! caracter to have the opposite
if [ ! -d "$DIR/Analysis/$case/Cortical_masks" ]
then
#Your code
fi
Question 02 :
Also, it just converts img to niig.gz for one folder at a time. First time you execute the script, converts imgs for the folder belonging to the first individual, etc
If you want to do two actions in the same time, why do you not create two bash scripts and execute them simulteanously ? Or, you can automate them by creating a process in your OS which will execute scripts for you.