Hi Rick,
Thanks for your suggestion, which is great!
Because I have 1 run for resting and 5 runs for task fMRI, I decided to generate another sub-folder for each run, and to save the outputs in those folders, in order to avoid overwriting. For this I am doing something like:
for ((i=1;i<133;i++)); do
mkdir 5.1st_level_analysis/sub-${i}
mkdir 5.1st_level_analysis/sub-${i}/func
mkdir 5.1st_level_analysis/sub-${i}/func/GLM_INPUT
for ((j=1; j<6; j++)); do
mkdir 5.1st_level_analysis/sub-${i}/func/GLM_INPUT/run-${j}
cd 5.1st_level_analysis/sub-${i}/func/GLM_INPUT/run-${j}
3dBlurToFWHM -input ${global_path}2.derivatives/sub-${i}/func/sub-${i}_task-stress_run-${j}_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz \
-prefix ${global_path}5.1st_level_analysis/sub-${i}/func/GLM_INPUT/sub-${i}_task-stress_run-${j}_space-MNI152NLin6Asym_res-2_desc-preproc_bold_blur.nii.gz \
-mask ${global_path}2.derivatives/sub-${i}/func/sub-${i}_task-stress_run-${j}_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz \
-FWHM 6 -detrend
done
done
Thanks for your useful help!
R. Nechifor.