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methods_tsnr.sh
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methods_tsnr.sh
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#$ -m be
#$ -m be
#$ -M [email protected]
#$ -S /bin/bash
module load afni/stable
method=$1
sub=$2
tsk=$3
task=tedana_${tsk}
analysis_windows=analysis_03-24
repo="/bcbl/home/public/MarcoMotion/scripts/HABLA_SPiN/"
target="/bcbl/home/public/MarcoMotion/Habla_restingState/${analysis_windows}/"
preproc="func_preproc_${method}/"
mkdir -p ${target}
origin="/bcbl/home/public/MarcoMotion/Habla_restingState/sub-00${sub}/ses-1/func_preproc_vanilla/"
root="/bcbl/home/public/MarcoMotion/Habla_restingState/sub-00${sub}/ses-1/${preproc}"
echo analizing subject sub-00${sub}
echo analizing task ${tsk}
mask=${origin}sub-00${sub}_ses-1_${tsk}_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
ln -s ${mask} ${ln_mask}
#OPTIMAL COMBINATION TSNR CALCULATION
3dTstat -mean -prefix ${root}${task}/desc-optcom_bold_mean.nii.gz ${root}${task}/desc-optcom_bold.nii.gz -overwrite
#Estimating spatial smoothness
3dFWHMx -geom -detrend -input ${root}${task}/desc-optcom_bold.nii.gz -mask ${ln_mask} -overwrite -out ${root}${task}/desc-optcom_bold_smoothness.1D
3dTproject -polort 5 -prefix ${root}${task}/desc-optcom_bold_dt.nii.gz -input ${root}${task}/desc-optcom_bold.nii.gz -overwrite
3dcalc -a ${root}${task}/desc-optcom_bold_dt.nii.gz -b ${root}${task}/desc-optcom_bold_mean.nii.gz -expr 'a+b' -prefix ${root}${task}/desc-optcom_bold_dt.nii.gz -overwrite
3dTstat -stdevNOD -prefix ${root}${task}/desc-optcom_bold_std.nii.gz ${root}${task}/desc-optcom_bold_dt.nii.gz -overwrite
3dcalc -a ${root}${task}/desc-optcom_bold_mean.nii.gz -b ${root}${task}/desc-optcom_bold_std.nii.gz -m ${mask} -expr 'm*(a/b)' -prefix ${root}${task}/desc-optcom_bold_tsnr_${method}.nii.gz -overwrite
ln -s ${root}${task}/desc-optcom_bold_tsnr_${method}.nii.gz ${target}sub-00${sub}_ses-1_${task}_desc-optcom_bold_tsnr_${method}.nii.gz
ln -s ${root}${task}/desc-optcom_bold_smoothness.1D ${target}sub-00${sub}_ses-1_${task}_desc-optcom_bold_tsnr_${method}.1D
##
## 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}/desc-optcomDenoised_bold_mean.nii.gz ${root}${task}/desc-optcomDenoised_bold.nii.gz -overwrite
#Estimating spatial smoothness
3dFWHMx -geom -detrend -input ${root}${task}/desc-optcomDenoised_bold.nii.gz -mask ${ln_mask} -overwriten -out ${root}${task}/desc-optcomDenoised_bold_smoothness.1D
3dTproject -polort 5 -prefix ${root}${task}/desc-optcomDenoised_bold_dt.nii.gz -input ${root}${task}/desc-optcomDenoised_bold.nii.gz -overwrite
3dcalc -a ${root}${task}/desc-optcomDenoised_bold_dt.nii.gz -b ${root}${task}/desc-optcomDenoised_bold_mean.nii.gz -expr 'a+b' -prefix ${root}${task}/desc-optcomDenoised_bold_dt.nii.gz -overwrite
3dTstat -stdevNOD -prefix ${root}${task}/desc-optcomDenoised_bold_std.nii.gz ${root}${task}/desc-optcomDenoised_bold_dt.nii.gz -overwrite
3dcalc -a ${root}${task}/desc-optcomDenoised_bold_mean.nii.gz -b ${root}${task}/desc-optcomDenoised_bold_std.nii.gz -m ${mask} -expr 'm*(a/b)' -prefix ${root}${task}/desc-optcomDenoised_bold_tsnr_${method}.nii.gz -overwrite
ln -s ${root}${task}/desc-optcomDenoised_bold_tsnr_${method}.nii.gz ${target}sub-00${sub}_ses-1_${task}_desc-optcomDenoised_bold_tsnr_${method}.nii.gz
ln -s ${root}${task}/desc-optcom_boldDenoised_bold_smoothness.1D ${target}sub-00${sub}_ses-1_${task}_desc-optcom_bold_tsnr_${method}.1D
echo TSNR calculation done for ${tasks} with ${method} method