compute_mu.sh

#!/bin/bash

# compute_mu.sh
#
# Computes the mean across each run within this sub-session, saves in align_QC directory
#
# (note: this is a super-slimmed-down version of the spatail_afni_proc_SEalign.sh that ONLY does the mean volume computation - used to re-run QC alone with preproc_QC.sh if necessary)
#
# DATAROOT is global variable now



EXPTDIR=$1

SUBJ=$2
SESS=$3

SEtarg=$4
STARTRUN=$5
ENDRUN=$6



cd $DATAROOT/$EXPTDIR/$SUBJ/$SESS/


#oldthreads=$(echo $OMP_NUM_THREADS)




#cd $DATAROOT/$EXPTDIR/$SUBJ/$SESS/
mkdir $DATAROOT/$EXPTDIR/$SUBJ/align_QC



# where do we put results?
RESULTSDIR=${SUBJ}_${SESS}_r${STARTRUN}to${ENDRUN}_SEalign


# must make STARTRUN; ENDRUN base10...$((10#$STARTRUN))

# loop from end to beginning of run list, converting all r## (1-n) to startrun:endrun
# runidx=$(( $((10#$ENDRUN)) - $((10#$STARTRUN)) + 1 ))
# for (( i=$((10#$ENDRUN)); i>=$((10#$STARTRUN)); i-- ))
# do
#   echo Renaming run $runidx to run $i

# # perl rename str   # rename -n -v 's/\.r02.(.*.)\./.r03.$1./' *.suff
#   repstr=s/`printf "\.r%02.f.(.*.)\." $runidx`/`printf ".r%02.f." $i`'$1'./
#   rename -v $repstr `printf "$RESULTSDIR.results/*.r%02.f.*" $runidx`

#   runidx=$(( $runidx - 1 ))
# done


# make QC files ($SUBJ/align_QC/$SUBJ_$SESS_mu_r$i.nii.gz)

# average over each run
for ii in $(seq -s " " $STARTRUN $ENDRUN)
do
  rnum=$(printf "%02.f" $ii)
  3dTstat -overwrite -mean -prefix ../align_QC/${SUBJ}_${SESS}_mu_r$rnum.nii.gz $RESULTSDIR.results/pb02.$RESULTSDIR.r$rnum.volreg+orig
done