#!/bin/bash

#rapidtide \
#    --nprocs -1 \
#    --passes 3 \
#    --refinetype unweighted_average \
#    --numnull 0 \
#    --outputlevel max \
#    --glmderivs 1 \
#    sub-RAPIDTIDETEST.nii.gz \
#    ../dst/sub-RAPIDTIDETEST

##retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/0deriv --nprocs -1 
retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/1deriv --nprocs -1 --glmderivs 1 --makepseudofile --outputlevel max
##retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/2deriv --nprocs -1 --glmderivs 2
##retroglm sub-RAPIDTIDETEST.nii.gz ../dst/sub-RAPIDTIDETEST --alternateoutput ../dst/3deriv --nprocs -1 --glmderivs 3

ALTNAME=1deriv

#for map in lfofilterR lfofilterR2 lfofilterMean lfofilterCoeff lfofilterCoeffDeriv1 lfofilterNorm lfofilterInbandVarianceBefore lfofilterInbandVarianceAfter lfofilterInbandVarianceChange 
#do
#    fslmaths \
#        ../dst/${ALTNAME}_desc-${map}_map.nii.gz \
#        -sub \
#        ../dst/sub-RAPIDTIDETEST_desc-${map}_map.nii.gz \
#        ../dst/diff_${map}
#    therange=`fslstats ../dst/diff_${map} -R`
#    echo ${map}: ${therange}
#done
#
##for map in processed_mask corrfit_mask maxtime_map
##do
##    readname=`echo ${map} | sed 's/_/READ_/g'`
##    fslmaths \
#        ../dst/${ALTNAME}_desc-${readname}.nii.gz \
#        -sub \
#        ../dst/sub-RAPIDTIDETEST_desc-${map}.nii.gz \
#        ../dst/diff_${map}
#    therange=`fslstats ../dst/diff_${map} -R`
#    echo ${map}: ${therange}
#done

#for map in datatofilter_bold
#do
    #fslmaths \
        #../dst/${ALTNAME}_desc-${map}.nii.gz \
        #-sub \
        #../dst/sub-RAPIDTIDETEST_desc-${map}.nii.gz \
        #../dst/diff_${map}
    #therange=`fslstats ../dst/diff_${map} -R`
    #echo ${map}: ${therange}
#done

#for map in lfofilterEV_bold lfofilterEVDeriv1_bold lfofilterRemoved_bold lfofilterCleaned_bold
#do
#    fslmaths \
#        ../dst/${ALTNAME}_desc-${map}.nii.gz \
#        -sub \
#        ../dst/sub-RAPIDTIDETEST_desc-${map}.nii.gz \
#        ../dst/diff_${map}
#    therange=`fslstats ../dst/diff_${map} -R`
#    echo ${map}: ${therange}
#done
#
