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1_trim.sh
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1_trim.sh
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#$ -m be
#$ -m be
#$ -M m.flores@bcbl.eu
#$ -S /bin/bash
module load afni/latest
method=cipactli
repo="/bcbl/home/public/MarcoMotion/scripts/HABLA_SPiN/"
target="/bcbl/home/public/MarcoMotion/Habla_restingState/OHBM_analysis_pre/"
preproc="func_preproc_hydra/"
mkdir -p ${target}
for sub in {1..5};do
origin="/bcbl/home/public/MarcoMotion/Habla_restingState/sub-00${sub}/ses-1/func_preproc/"
root="/bcbl/home/public/MarcoMotion/Habla_restingState/sub-00${sub}/ses-1/${preproc}"
for task in task-HABLA1200 task-HABLA1700;do
for n_echo in {1..4};do
#for oc in desc-optcom desc-optcomDenoised;do
echo analizing subject sub-00${sub}
echo analizing task ${task}
mask=${origin}sub-00${sub}_ses-1_${task}_echo-1_part-mag_brain_mask.nii.gz
ln_mask=${target}sub-00${sub}_ses-1_${task}_echo-1_part-mag_brain_mask.nii.gz
#OPTIMAL COMBINATION TSNR CALCULATION
3dTstat -mean -prefix ${root}sub-00${sub}_ses-1_${task}_echo-${n_echo}_part-mag_bold_${method}_mcf_al.nii.gz ${root}${task}brain_mask/${oc}_bold.nii.gz -overwrite
3dTproject -polort 5 -prefix ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -input ${root}${task}brain_mask/${oc}_bold.nii.gz -overwrite
3dcalc -a ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -b ${root}${task}brain_mask/${oc}_bold_mean.nii.gz -expr 'a+b' -prefix ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -overwrite
3dTstat -stdevNOD -prefix ${root}${task}brain_mask/${oc}_bold_std.nii.gz ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -overwrite
3dcalc -a ${root}${task}brain_mask/${oc}_bold_mean.nii.gz -b ${root}${task}brain_mask/${oc}_bold_std.nii.gz -m ${mask} -expr 'm*(a/b)' -prefix ${root}${task}brain_mask/${oc}_bold_tsnr_${method}.nii.gz -overwrite
ln -s ${root}${task}brain_mask/${oc}_bold_tsnr_${method}.nii.gz ${target}sub-00${sub}_${task}${oc}_bold_tsnr_${method}.nii.gz
##
## TODO: quitar la segunda parte. Anidar lo de abajo en . Reiterar.
## La creación de links se mantiene.
##
#DENOISED OPTIMAL COMBINATION TSNR CALCULATION
#3dTstat -mean -prefix ${root}${task}brain_mask/${oc}_bold_mean.nii.gz ${root}${task}brain_mask/${oc}_bold.nii.gz -overwrite
#3dTproject -polort 5 -prefix ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -input ${root}${task}brain_mask/${oc}_bold.nii.gz -overwrite
#3dcalc -a ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -b ${root}${task}brain_mask/${oc}_bold_mean.nii.gz -expr 'a+b' -prefix ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -overwrite
#3dTstat -stdevNOD -prefix ${root}${task}brain_mask/${oc}_bold_std.nii.gz ${root}${task}brain_mask/${oc}_bold_dt.nii.gz -overwrite
#3dcalc -a ${root}${task}brain_mask/${oc}_bold_mean.nii.gz -b ${root}${task}brain_mask/${oc}_bold_std.nii.gz -m ${mask} -expr 'm*(a/b)' -prefix ${root}${task}brain_mask/${oc}_bold_tsnr_${method}.nii.gz -overwrite
#ln -s ${root}${task}brain_mask/${oc}_bold_tsnr_${method}.nii.gz ${target}sub-00${sub}_${task}${oc}_bold_tsnr_${method}.nii.gz
ln -s ${mask} ${ln_mask}
echo TSNR calculation done for ${tasks} with ${method} method
done
done
done