dual_regression

#!/bin/sh

#   dual_regression - take group-ICA maps (etc) and get subject-specific versions of them (and associated timecourses)
#
#   Stephen Smith, Christian Beckmann, Janine Bijsterbosch, Sam Harrison, FMRIB Image Analysis Group
#
#   Copyright (C) 2011-2019 University of Oxford
#
#   SHCOPYRIGHT

export LC_ALL=C

Usage() {
    cat <<EOF

dual_regression v0.6

***NOTE*** ORDER OF COMMAND-LINE ARGUMENTS IS DIFFERENT FROM PREVIOUS VERSION

Usage: dual_regression <group_IC_maps> <des_norm> <design.mat> <design.con> <n_perm> [--thr] <output_directory> <input1> <input2> <input3> .........
e.g.   dual_regression groupICA.gica/groupmelodic.ica/melodic_IC 1 design.mat design.con 500 0 grot \`cat groupICA.gica/.filelist\`

<group_IC_maps_4D>            4D image containing spatial IC maps (melodic_IC) from the whole-group ICA analysis
<des_norm>                    0 or 1 (1 is recommended). Whether to variance-normalise the timecourses used as the stage-2 regressors
<design.mat>                  Design matrix for final cross-subject modelling with randomise
<design.con>                  Design contrasts for final cross-subject modelling with randomise
<n_perm>                      Number of permutations for randomise; set to 1 for just raw tstat output, set to 0 to not run randomise at all.
[--thr]                       Perform thresholded dual regression to obtain unbiased timeseries for connectomics analyses (e.g., with FSLnets)
<output_directory>            This directory will be created to hold all output and logfilesg
<input1> <input2> ...         List all subjects' preprocessed, standard-space 4D datasets

<design.mat> <design.con>     can be replaced with just
-1                            for group-mean (one-group t-test) modelling.
If you need to add other randomise options then edit the line after "EDIT HERE" in the dual_regression script

EOF
    exit 1
}

############################################################################

[ "$6" = "" ] && Usage

ORIG_COMMAND=$*

ICA_MAPS=`${FSLDIR}/bin/remove_ext $1` ; shift

DES_NORM=--des_norm
if [ $1 = 0 ] ; then
  DES_NORM=""
fi ; shift

if [ $1 = "-1" ] ; then
  DESIGN="-1"
  shift
else
  dm=$1
  dc=$2
  DESIGN="-d $1 -t $2"
  shift 2
fi

NPERM=$1 ; shift

NAF2=0
if [ $1 = "--thr" ] ; then
  NAF2=1
  shift
fi

OUTPUT=`${FSLDIR}/bin/remove_ext $1` ; shift

while [ _$1 != _ ] ; do
  INPUTS="$INPUTS `${FSLDIR}/bin/remove_ext $1`"
  shift
done

############################################################################

mkdir $OUTPUT
LOGDIR=${OUTPUT}/scripts+logs
mkdir $LOGDIR
echo $ORIG_COMMAND > $LOGDIR/command
if [ "$DESIGN" != -1 ] ; then
  /bin/cp $dm $OUTPUT/design.mat
  /bin/cp $dc $OUTPUT/design.con
fi

echo "creating common mask"
j=0
for i in $INPUTS ; do
  echo "$FSLDIR/bin/fslmaths $i -Tstd -bin ${OUTPUT}/mask_`${FSLDIR}/bin/zeropad $j 5` -odt char" >> ${LOGDIR}/drA
  j=`echo "$j 1 + p" | dc -`
done
ID_drA=`$FSLDIR/bin/fsl_sub -T 10 -N mask_generation1 -l $LOGDIR -t ${LOGDIR}/drA`
cat <<EOF > ${LOGDIR}/drB
#!/bin/sh
\$FSLDIR/bin/fslmerge -t ${OUTPUT}/maskALL \`\$FSLDIR/bin/imglob ${OUTPUT}/mask_*\`
\$FSLDIR/bin/fslmaths $OUTPUT/maskALL -Tmin $OUTPUT/mask
\$FSLDIR/bin/imrm $OUTPUT/mask_*
EOF
chmod a+x ${LOGDIR}/drB
ID_drB=`$FSLDIR/bin/fsl_sub -j $ID_drA -T 5 -N mask_generation2 -l $LOGDIR ${LOGDIR}/drB`

echo "doing the dual regressions"
j=0
for i in $INPUTS ; do
  s=subject`${FSLDIR}/bin/zeropad $j 5`
  echo "$FSLDIR/bin/fsl_glm -i $i -d $ICA_MAPS -o $OUTPUT/dr_stage1_${s}.txt --demean -m $OUTPUT/mask ; \
        $FSLDIR/bin/fsl_glm -i $i -d $OUTPUT/dr_stage1_${s}.txt -o $OUTPUT/dr_stage2_$s --out_z=$OUTPUT/dr_stage2_${s}_Z --demean -m $OUTPUT/mask $DES_NORM ; \
        $FSLDIR/bin/fslsplit $OUTPUT/dr_stage2_$s $OUTPUT/dr_stage2_${s}_ic" >> ${LOGDIR}/drC
  j=`echo "$j 1 + p" | dc -`
done
ID_drC=`$FSLDIR/bin/fsl_sub -j $ID_drB -T 30 -N dual_regression -l $LOGDIR -t ${LOGDIR}/drC`

if [ $NAF2 -eq 1 ] ; then
   echo "doing thresholded dual regression"
   echo "1" > ${OUTPUT}/tmp.txt
   j=0
   for i in $INPUTS ; do
      s=subject`${FSLDIR}/bin/zeropad $j 5`
      echo "$FSLDIR/bin/melodic -i ${OUTPUT}/dr_stage2_${s} --ICs=${OUTPUT}/dr_stage2_${s} --mix=${OUTPUT}/tmp.txt -o ${OUTPUT}/MM_${s} --Oall --report -v --mmthresh=0" >> ${LOGDIR}/drD1
      echo "$FSLDIR/bin/fslmerge -t ${OUTPUT}/MM_${s}/stats/thresh2 \`\$FSLDIR/bin/imglob ${OUTPUT}/MM_${s}/stats/thresh_zstat?.* ${OUTPUT}/MM_${s}/stats/thresh_zstat??.* ${OUTPUT}/MM_${s}/stats/thresh_zstat???.*\` ; sleep 10 ; \
	    $FSLDIR/bin/imrm \`\$FSLDIR/bin/imglob ${OUTPUT}/MM_${s}/stats/thresh_zstat*.*\` ; \
	    cp ${OUTPUT}/MM_${s}/stats/thresh2.nii.gz ${OUTPUT}/MM_${s}/stats/thresh2_negative.nii.gz ; \
	    cp ${OUTPUT}/MM_${s}/stats/thresh2.nii.gz ${OUTPUT}/MM_${s}/stats/thresh2_positive.nii.gz ; \
	    $FSLDIR/bin/fslmaths ${OUTPUT}/MM_${s}/stats/thresh2_negative -uthr -2 ${OUTPUT}/MM_${s}/stats/thresh2_negative ; \
	    $FSLDIR/bin/fslmaths ${OUTPUT}/MM_${s}/stats/thresh2_positive -thr 2 ${OUTPUT}/MM_${s}/stats/thresh2_positive ; \
	    $FSLDIR/bin/fslmaths ${OUTPUT}/MM_${s}/stats/thresh2_negative -add ${OUTPUT}/MM_${s}/stats/thresh2_positive ${OUTPUT}/MM_${s}/stats/thresh2 ; \
            $FSLDIR/bin/imrm \`\$FSLDIR/bin/imglob ${OUTPUT}/MM_${s}/stats/thresh2_*.*\` ; \
	    $FSLDIR/bin/fsl_glm -i $i -d ${OUTPUT}/MM_${s}/stats/thresh2 -o $OUTPUT/dr_stage4_${s}.txt --demean -m $OUTPUT/mask" >> ${LOGDIR}/drD2
      j=`echo "$j 1 + p" | dc -`
   done
   ID_drD1=`$FSLDIR/bin/fsl_sub -j $ID_drC -N mixture_model -l $LOGDIR -t ${LOGDIR}/drD1`
   ID_drD2=`$FSLDIR/bin/fsl_sub -j $ID_drD1 -N thresholdedDR -l $LOGDIR -t ${LOGDIR}/drD2`
fi

echo "sorting maps and running randomise"
j=0
Nics=`$FSLDIR/bin/fslnvols $ICA_MAPS`
while [ $j -lt $Nics ] ; do
  jj=`$FSLDIR/bin/zeropad $j 4`

  RAND=""
  if [ $NPERM -eq 1 ] ; then
    RAND="$FSLDIR/bin/randomise -i $OUTPUT/dr_stage2_ic$jj -o $OUTPUT/dr_stage3_ic$jj -m $OUTPUT/mask $DESIGN -n 1 -V -R"
  fi
  if [ $NPERM -gt 1 ] ; then
    # EDIT HERE
    RAND="$FSLDIR/bin/randomise -i $OUTPUT/dr_stage2_ic$jj -o $OUTPUT/dr_stage3_ic$jj -m $OUTPUT/mask $DESIGN -n $NPERM -T -V"
  fi

  echo "$FSLDIR/bin/fslmerge -t $OUTPUT/dr_stage2_ic$jj \`\$FSLDIR/bin/imglob $OUTPUT/dr_stage2_subject*_ic${jj}.*\` ; \
        $FSLDIR/bin/imrm \`\$FSLDIR/bin/imglob $OUTPUT/dr_stage2_subject*_ic${jj}.*\` ; $RAND" >> ${LOGDIR}/drE
  j=`echo "$j 1 + p" | dc -`
done
ID_drE=`$FSLDIR/bin/fsl_sub -j $ID_drC -T 60 -N randomise -l $LOGDIR -t ${LOGDIR}/drE`