Hello
I am using FSL to extract timeseries from FMRI at one ROI at a time and am facing issues while scaling up this process. I there any way i can extract timeseries at all the locations simultaneously.
The script that i am using rn for extracting timeseries:
#!/bin/bash
#script name : ts_extract_CN.sh
base_dir="path/CNStandard_name"
for i in CB DMN FP OP CO SM; do
file_path="path/DoschenbachROI/$i.txt"
for subject_dir in "$base_dir"/*.feat; do
if [[ -d "$subject_dir" ]]; then
subject_name=$(basename "$subject_dir")
echo $subject_name
cd "$base_dir/$subject_name"
subject_name1=$(basename "$subject_dir" .feat)
output_file="${subject_name1}_${i}.csv"
counter=0
while read line; do
IFS=',' read -r centerx centery centerz <<< "$line"
counter=$((counter+1))
fslmaths roi_template.nii.gz -mul 0 -add 1 -roi $centerx 1 $centery 1 $centerz 1 0 1 ACCpoint -odt float
fslmaths ACCpoint -kernel sphere 5 -fmean ACCsphere_$counter -odt float
fslmaths ACCsphere_$counter.nii.gz -bin ACCsphere_bin_$counter.nii.gz
roi_timeseries=$(fslmeants -i res_brain_std -m ACCsphere_bin_$counter)
time_series="$roi_timeseries"
echo "$time_series" >> $output_file
done < $file_path
rm -r ACC*
fi
done
done