added

dual_regression

+#!/bin/sh
+
+#   dual_regression - take group-ICA maps (etc) and get subject-specific versions of them (and associated timecourses)
+#
+#   Stephen Smith and Christian Beckmann, FMRIB Image Analysis Group
+#
+#   Copyright (C) 2011-2012 University of Oxford
+#
+#   SHCOPYRIGHT
+
+
+Usage() {
+    cat <<EOF
+
+dual_regression v0.5 (beta)
+
+***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> <output_directory> <input1> <input2> <input3> .........
+e.g.   dual_regression groupICA.gica/groupmelodic.ica/melodic_IC 1 design.mat design.con 500 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.
+<output_directory>            This directory will be created to hold all output and logfiles
+<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 option then just edit the line after "EDIT HERE" below
+
+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=$1 ; shift
+
+OUTPUT=`${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 drA -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 drB -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 drC -l $LOGDIR -t ${LOGDIR}/drC`
+
+echo "sorting maps and running randomise"
+j=0
+Nics=`$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" >> ${LOGDIR}/drD
+  j=`echo "$j 1 + p" | dc -`
+done
+ID_drD=`$FSLDIR/bin/fsl_sub -j $ID_drC -T 60 -N drD -l $LOGDIR -t ${LOGDIR}/drD`
+