#!/bin/csh -f

#happy \
#    ~/Dropbox_PHC/MR_data_2/physioconn/rfMRI_REST1_LR/100206_3T_rfMRI_REST1_LR.nii.gz \
#    ~/Dropbox_PHC/MR_data_2/physioconn/rfMRI_REST1_LR/slicetimes.txt \
#    ~/Dropbox_PHC/MR_data_2/physioconn/happytest/happyarm \
#    --mklthreads -1 \
#    --infotag tag1 value1 \
#    --infotag tag2 value2 \
#    --model model_revised

happy \
    sub-HAPPYTEST.nii.gz \
    sub-HAPPYTEST.json \
    ../dst/happy \
    --mklthreads 8 \
    --model model_revised \
    --spatialglm --aliasedcorrelation


#happy \
#    sub-HAPPYTEST.nii.gz \
#    sub-HAPPYTEST.json \
#    ../dst/happy_2comp \
#    --cardiacfile happystdres_bids.tsv:normcardiac_25.0Hz \
#    --mklthreads 8 \
#    --hilbertcomponents 2 \
#    --model model_revised
#
#happy \
#    sub-HAPPYTEST.nii.gz \
#    sub-HAPPYTEST.json \
#    ../dst/happy_3comp \
#    --cardiacfile happystdres_bids.tsv:normcardiac_25.0Hz \
#    --mklthreads 8 \
#    --hilbertcomponents 3 \
#    --model model_revised

#happy_legacy \
    #sub-HAPPYTEST.nii.gz \
    #sub-HAPPYTEST.json \
    #../dst/happy_normaltest \
    #--mklthreads=8 \
    #--model=model_revised \
    #--outputbins=40 \
    #--gridbins=3.5 \
    #--stdfreq=20.0 \
    #--estmask=happytestvesselmask.nii.gz \
    #--minhr=46 \
    #--maxhr=131.2 \
    #--minhrfilt=45.5 \
    #--maxhrfilt=800.0 \
    #--envcutoff=0.45 \
    #--notchwidth=1.25 \
    #--cardiacfile=happytestpleth.txt \
    #--cardiacfreq=20.0 \
    #--cardiacstart=0.0 \
    #--aliasedcorrelation \
    #--increaseoutputlevel \
    #--increaseoutputlevel \
    #--decreaseoutputlevel \
    #--dodlfilter


#happy \
    #ses-060_bold_trunc.nii.gz \
    #ses-060_bold_trunc.json \
    #../dst/happy_motion \
    #--mklthreads 8 \
    #--motionfile ses-060_bold_trunc_prefiltered_func_data_mcf.par
