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fit_tensor_report.sh
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#! /bin/sh
usage_exit() {
cat <<EOF
Generates report for the tensor fitting procedure
Usage:
$CMD -t <directory with intermediate files from unwarp_fieldmap> -r <directory to put the generated reports> -o <output directory> -k <input 4D dti file> -m <method used> -n <number of b0 volumes>
EOF
exit 1;
}
#---------variables and defaults---------#
tmpdir=temp-fit_tensor # name of directory for intermediate files
reportdir=fit_tensor_report # report dir
logfile_name=fit_tensor_report.log # Log file
method=restore
outdir=.
dti=DTI_64.nii.gz
scriptdir=`dirname $0`
s0_count=2
#----------- Utility Functions ----------#
T () {
E=0
if [ "$1" = "-e" ] ; then # just outputting and logging a message with T -e
E=1; shift
fi
cmd="$*"
echo $* | tee -a $LF # read the command into the console, and the log file
if [ "$E" != "1" ] ; then
$cmd 2>&1 | tee -a $LF # run the command. read the output into a the log file. Stderr is not directed to the logfile
fi
echo | tee -a $LF # write an empty line to the console and log file
}
error_exit (){
echo "$1" >&2 # Send message to stderr
echo "$1" >> $LF # send message to log file
exit "${2:-1}" # Return a code specified by $2 or 1 by default.
}
#------------- Parse Parameters --------------------#
while getopts t:r:s:o:k:m:n: OPT
do
case "$OPT" in
"t" ) tmpdir="$OPTARG";;
"r" ) reportdir="$OPTARG";;
"o" ) outdir="$OPTARG";;
"k" ) dti="$OPTARG";;
"m" ) method="$OPTARG";;
"n" ) s0_count="$OPTARG";;
* ) usage_exit;;
esac
done;
#------------- Setting things up --------------------#
LF=$reportdir/$logfile_name
RF=$reportdir/fit_tensor_report
if [ -e $reportdir ]; then /bin/rm -Rf $reportdir;fi
mkdir -p $reportdir
#------------- Check dependencies ----------------#
command -v fsl > /dev/null 2>&1 || { error_exit "ERROR: FSL required for report, but not found (http://fsl.fmrib.ox.ac.uk/fsl). Aborting."; }
command -v whirlgif > /dev/null 2>&1 || command -v gifsicle > /dev/null 2>&1 || { error_exit "ERROR: either whirlgif or gifsicle required for report, but neither found. Aborting."; }
command -v pandoc > /dev/null 2>&1 || { error_exit "ERROR: pandoc required for report, but not found (http://pandoc.org/). Aborting."; }
command -v R > /dev/null 2>&1 || { error_exit "ERROR: R required for report, but not found (https://www.r-project.org). Aborting."; }
rmarkdown_test=`R -q -e "\"rmarkdown\" %in% rownames(installed.packages())" | grep 1`
if [ "$rmarkdown_test" != "[1] TRUE" ]; then error_exit "ERROR: R package 'rmarkdown' required for report, but not found.
Try running this command in R:
install.packages(\"rmarkdown\") " ;fi
#------------- Begin report --------------------#
echo "---"> ${RF}.Rmd
echo "title: QA report for tensor fitting as part of DTI preprocessing ">> ${RF}.Rmd
echo "output:" >> ${RF}.Rmd
echo " html_document: " >> ${RF}.Rmd
echo " keep_md: yes " >> ${RF}.Rmd
echo " toc: yes " >> ${RF}.Rmd
echo " force_captions: TRUE " >> ${RF}.Rmd
echo "---">> ${RF}.Rmd
echo \# FIT TENSOR REPORT >> ${RF}.Rmd
echo "__tensor fitting method: $method __\n" >> ${RF}.Rmd
## FA
echo "## FA Image " >> ${RF}.Rmd
T $scriptdir/image_to_gif.sh $outdir/dti_FA.nii.gz $reportdir/fa.gif
echo " \n" >> ${RF}.Rmd
## MD
echo "## MD Image" >> ${RF}.Rmd
T $scriptdir/image_to_gif.sh $outdir/dti_MD.nii.gz $reportdir/md.gif
echo " \n" >> ${RF}.Rmd
if [ "$method" = "restore" ]; then
## Outlier count
T fslhd $dti | grep ^dim1 | awk '{print $2}'
T fslhd $dti | grep ^dim2 | awk '{print $2}'
T fslhd $dti | grep ^dim3 | awk '{print $2}'
xdim=`fslhd $dti | grep ^dim1 | awk '{print $2}'`
ydim=`fslhd $dti | grep ^dim2 | awk '{print $2}'`
zdim=`fslhd $dti | grep ^dim3 | awk '{print $2}'`
echo "##Outliers across volumes" >> ${RF}.Rmd
T fslmaths $tmpdir/dti_outlier_map.nii.gz -Xmean -Ymean -Zmean -mul $xdim -mul $ydim -mul $zdim $reportdir/outlier_ts_avg
T tsplot $reportdir/tsplot_temp -f $reportdir/outlier_ts_avg.nii.gz -C 0 0 0 $reportdir/outliers_ts.txt
cat $reportdir/outliers_ts.txt | tail -n +`echo $s0_count+1|bc` > $reportdir/outliers_ts_trim.txt
T fsl_tsplot -i $reportdir/outliers_ts_trim.txt -o $reportdir/outlier_plot.png -t Outliers -x Volume
echo " \n" >> ${RF}.Rmd
## outlier count across volumes
echo "## Outlier Image " >> ${RF}.Rmd
T $scriptdir/image_to_gif.sh $tmpdir/dti_outlier_count.nii.gz $reportdir/outlier_count.gif
echo " \n" >> ${RF}.Rmd
## Sigma
sigma=`fslstats $tmpdir/sigma_map -P 50`
echo "__Median noise level across the image: $sigma __ \n" >> ${RF}.Rmd
# log S0
echo "## log - S0 Image " >> ${RF}.Rmd
T fslmaths $tmpdir/dti_log_s0.nii.gz -mas $tmpdir/dti_MD.nii.gz $tmpdir/dti_log_s0_mas.nii.gz
T $scriptdir/image_to_gif.sh $tmpdir/dti_log_s0_mas.nii.gz $reportdir/S0.gif
echo " \n" >> ${RF}.Rmd
## noise map
#echo "<B>Noise Image </B><BR>" >> ${RF}.Rmd
#image_to_gif $tmpdir/noise_map.nii.gz $reportdir/noise.gif
#echo "<IMG src="./noise.gif" width="1200" height="100" border="0"><BR><BR>" >> ${RF}.Rmd
fi
if [ "$method" = "fsl" ]; then
# S0
echo "## S0 Image " >> ${RF}.Rmd
T $scriptdir/image_to_gif.sh $tmpdir/dti_S0.nii.gz $reportdir/S0.gif
echo " \n" >> ${RF}.Rmd
#SSE
echo "## Sum-squared error Image " >> ${RF}.Rmd
T $scriptdir/image_to_gif.sh $tmpdir/dti_sse.nii.gz $reportdir/SSE.gif
echo " \n" >> ${RF}.Rmd
fi
T R -e library\(rmarkdown\)\;rmarkdown::render\(\"${RF}.Rmd\"\)