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echo "It starts now"
3dTstat -mean -prefix mean_nulled.nii $1'[1..$(2)]' -overwrite
3dTstat -mean -prefix mean_notnulled.nii $1'[0..$(2)]' -overwrite
# Run motion correction. Athought I originally did this on BOLD and Null together,
# I separated them here since these are the final BOLD time series & I'd need to make
# a distinct run for these data anyway.
NumVol=`3dinfo -nv $1`
echo "NumVol of BOLD is '$NumVol' "
3dcalc -overwrite -prefix Nulled.nii -a $1'[1..'`expr $NumVol - 2`'(2)]' -expr 'a'
3dcalc -overwrite -prefix NotNulled.nii -a $1'[0..'`expr $NumVol - 3`'(2)]' -expr 'a'
#renzo learn how to do moc with motionmask
3dvolreg -overwrite -prefix BOLD.volreg.nii -base mean_notnulled.nii -1Dmatrix_save BOLDmatri -dfile BOLD.dfile.1D -1Dfile BOLD.mot.1D -quitic NotNulled.nii
3dvolreg -overwrite -prefix Nulled.volreg.nii -base mean_nulled.nii -1Dmatrix_save Nulledmatri -dfile Nulled.dfile.1D -1Dfile Nulled.mot.1D -quitic Nulled.nii
rm mean_nulled.nii
rm mean_notnulled.nii
gnuplot "./gnuplot_moco_afni.txt"
echo "Calculate VASO!"
# Calculate VASO!
# The first vaso volume is first nulled volume divided by the 2nd BOLD volume
NumVol=`3dinfo -nv BOLD.volreg.nii`
3dcalc -prefix tmp.VASO_vol1.nii \
-a BOLD.volreg.nii'[0]' \
-b Nulled.volreg.nii'[0]' \
-expr 'b/a' -overwrite
3dcalc -prefix tmp.VASO_volend.nii \
-a BOLD.volreg.nii'['`expr $NumVol - 1`']' \
-b Nulled.volreg.nii'['`expr $NumVol - 1`']' \
-expr 'b/a' -overwrite
# Calculate all VASO volumes after the first one
# -a goes from the 2nd BOLD volume to the 2nd-to-last BOLD volume
# -b goes from the 3rd BOLD volume to the last BOLD volume
# -c goes from the 2nd Nulled volume to the last Nulled volume
NumVol=`3dinfo -nv BOLD.volreg.nii`
3dcalc -prefix VASO.volreg.nii \
-a BOLD.volreg.nii'[0..'`expr $NumVol - 2`']' \
-b BOLD.volreg.nii'[1..'`expr $NumVol - 1`']' \
-c Nulled.volreg.nii'[0..'`expr $NumVol - 2`']' \
-expr 'c*2/(a+b)' -overwrite
# concatinate the first VASO volume with the rest of the sequence
# 3dTcat -overwrite -prefix VASO.volreg.nii tmp.VASO_othervols.nii tmp.VASO_volend.nii
# Remove the temporary seprate files for the first VASO volume and the rest of the VASO volumes
#srm tmp.VASO_vol1*.nii tmp.VASO_othervols*.nii
# BOLD and VASO now have 3s or 312s TRs
# Use 3drefit to make this change in the file headers
3drefit -TR 3.0 VASO.volreg.nii
3drefit -TR 3.0 BOLD.volreg.nii
#echo ' remove last time point in BOLD'
NumVol=`3dinfo -nv BOLD.volreg.nii `
echo "NumVol of BOLD is '$Numvol' "
3dcalc -prefix BOLD.volreg.nii \
-a BOLD.volreg.nii'[0..'`expr $NumVol - 2`']' \
-expr 'a' -overwrite
#echo ' remove last time point in BOLD'
3dTstat -overwrite -mean -prefix MEAN_BOLD.nii \
3dTstat -overwrite -cvarinv -prefix tSNR_BOLD.nii \
3dTstat -overwrite -mean -prefix MEAN_VASO.nii \
3dTstat -overwrite -cvarinv -prefix tSNR_VASO..nii \
3dTstat -overwrite -mean -prefix MEAN_Nulled.nii \
3dTstat -overwrite -cvarinv -prefix tSNR_Nulled.nii \
3dcalc -prefix T1_like.nii \
-a MEAN_BOLD.nii \
-b MEAN_Nulled.nii \
-expr '(a+b)/(a-b)' -overwrite
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