Merge pull request #109 from jdkent/shellcheck

[MAINT] Shellcheck

Author: jdkent

.circleci/ds005_compcor.txt

@@ -280,7 +280,6 @@
 /sub-01/rot_mm.png
 /sub-01/rot.png
 /sub-01/rot_trans.png
-/sub-01/rsParam
 /sub-01/rsParams
 /sub-01/rsParams_log
 /sub-01/run_motionscrub.m
@@ -304,7 +303,6 @@
 /sub-01/seedCorrelation/compcor/rois/seedQC/UIUC_VIS_rvis_underlay_coronal.nii
 /sub-01/seedCorrelation/compcor/rois/seedQC/UIUC_VIS_rvis_underlay_sagittal.nii
 /sub-01/seedCorrelation/compcor/rois/seeds_forQC.txt
-/sub-01/seedCorrelation/compcor/rois/seeds_ms.txt
 /sub-01/seedCorrelation/compcor/rois/seeds.txt
 /sub-01/seedCorrelation/compcor/rois/UIUC_VIS_lvis_mask.nii.gz
 /sub-01/seedCorrelation/compcor/rois/UIUC_VIS_lvis_residvol_ms_ts.txt

.circleci/ds005_compcor_global.txt

@@ -132,7 +132,6 @@
 /sub-01/rot_mm.png
 /sub-01/rot.png
 /sub-01/rot_trans.png
-/sub-01/rsParam
 /sub-01/rsParams
 /sub-01/rsParams_log
 /sub-01/run_motionscrub.m

.travis.yml

@@ -1,5 +1,3 @@
-language: bash
-before_install:
-  - wget -c https://goo.gl/ZzKHFv -O - | tar -xvJ -C /tmp/
-  - PATH="/tmp/shellcheck-latest:$PATH"
-script: ./tests/shellcheck.sh
+language: shell
+script: 
+  - bash -c 'shopt -s globstar; shellcheck **/*.sh'

PlotPow.sh

@@ -15,7 +15,7 @@
 
 shopt -s nullglob # No-match globbing expands to null
 TmpDir=/tmp
-Tmp=$TmpDir/`basename $0`-${$}-
+Tmp=$TmpDir/$(basename "$0")-${$}-
 trap CleanUp INT
 
 ###############################################################################
@@ -26,7 +26,7 @@ trap CleanUp INT
 
 Usage() {
 cat <<EOF
-Usage: `basename $0` [options] 4Dimage mask PlotNm
+Usage: $(basename "$0") [options] 4Dimage mask PlotNm
 
 Within mask voxels, computes power spectrum at each point in 4Dimage, creating a
 plot in file PlotNm.png.  Image is always demeaned before computing the powerspectrum; 
@@ -47,7 +47,7 @@ exit
 }
 
 CleanUp () {
-    /bin/rm -f ${Tmp}*
+    /bin/rm -f "${Tmp}*"
     exit 0
 }
 
@@ -60,6 +60,7 @@ CleanUp () {
 
 TR=1
 Units=""
+VarNorm=0
 while (( $# > 1 )) ; do
     case "$1" in
         "-help")
@@ -132,13 +133,13 @@ fi
 
 # High pass?
 if [ "$HighPass" = "1" ] ; then
-    HPsigma=$(echo 100/2/$TR | bc -l)
+    HPsigma=$(echo 100/2/"$TR" | bc -l)
     fslmaths "$Img" -bptf "$HPsigma" -1 $Tmp-HPf
     Img=$Tmp-HPf
 fi
 
 # Center and possibly variance normalize 
-if [ "$VolNorm" = "1" ] ; then
+if [ "$VarNorm" = "1" ] ; then
     fslmaths "$Img" -Tstd $Tmp-sd -odt float
     fslmaths "$Img" -sub $Tmp-mean -div $Tmp-sd -mas "$Mask" $Tmp-img -odt float 
 else
@@ -150,9 +151,9 @@ fslpspec $Tmp-img  $Tmp-pspec
 
 # Make the plot
 fslmeants -i $Tmp-pspec -m $Tmp-mean -o "$Plot".txt
-Len=$(cat "$Plot".txt | wc -l )
+Len=$(wc -l < "$Plot".txt)
 Nyq=$(echo "0.5/$TR/$Len" | bc -l);
-fsl_tsplot -i "$Plot".txt -u $Nyq -t "$(basename $Plot)" -y "Power" -x "Frequency$Units" -o "$Plot".png
+fsl_tsplot -i "$Plot".txt -u "$Nyq" -t "$(basename "$Plot")" -y "Power" -x "Frequency$Units" -o "$Plot".png
 
 
 ###############################################################################

ROIs/Schaefer2018_LocalGlobal_MNI/Schaefer2018_400Parcels_17Networks/split400.sh

@@ -3,12 +3,12 @@
 #mwvoss script to split 400 parcellation to separate mask files
 #
 
-rows=`wc Schaefer2018_400Parcels_17Networks_order.txt | awk '{print $1;}'`
+rows=$(wc Schaefer2018_400Parcels_17Networks_order.txt | awk '{print $1;}')
 
-for (( i=1; i<=$rows; i++ )) ; do
-	parcel=`cat Schaefer2018_400Parcels_17Networks_order.txt | tr -s ' ' | awk -v i=$i 'FNR==i { print $2 }'`
-	echo $i $parcel
-	fslmaths Schaefer2018_400Parcels_17Networks_order_FSLMNI152_2mm.nii.gz -thr $i -uthr $i $parcel
+for (( i=1; i<=rows; i++ )) ; do
+	parcel=$(tr -s ' ' < Schaefer2018_400Parcels_17Networks_order.txt | awk -v i=$i 'FNR==i { print $2 }')
+	echo $i "$parcel"
+	fslmaths Schaefer2018_400Parcels_17Networks_order_FSLMNI152_2mm.nii.gz -thr $i -uthr $i "$parcel"
 	# JK: note ^^ probably want to add -bin after -uthr $i to the command, I'll
 	# make a more formal request as soon as this file is under version control. 
 done

makeROI_Noise.sh

@@ -24,6 +24,6 @@ outputImage=$4
 
 # ROI is arbitrarily set to %age of xy voxel dimensions ($2)
 
-fslmaths $inputImage -mul 0 -add 1 -roi 0 -1 ${1} 1 0 -1 0 1 $outputImage -odt float
-fslmaths $outputImage -kernel sphere $2 -fmean $outputImage -odt float
-fslmaths $outputImage -bin $outputImage
+fslmaths "$inputImage" -mul 0 -add 1 -roi 0 -1 "${1}" 1 0 -1 0 1 "$outputImage" -odt float
+fslmaths "$outputImage" -kernel sphere "$2" -fmean "$outputImage" -odt float
+fslmaths "$outputImage" -bin "$outputImage"

makeROI_batch.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 # feed csv of ROI coordinates to make seeds
 # run while in RestingState scripts directory
-scriptPath=$(perl -e 'use Cwd "abs_path";print abs_path(shift)' $0)
-Path=$(dirname $scriptPath)
-echo $Path
-cd $Path
+scriptPath=$(perl -e 'use Cwd "abs_path";print abs_path(shift)' "$0")
+Path=$(dirname "$scriptPath")
+echo "$Path"
+cd "$Path" || exit
 
 # example csv setup: net	x	y	z	diameter	seed	StudyOrigin
 #                    DMN	6      -60	32	14	        rPCC	  UIUC
@@ -17,33 +17,33 @@ Usage() {
 [ "$1" = "" ] && Usage
 
 
-inDir=$(dirname ${1})
-if [ -e $inDir/runseeds.txt ]; then
-   rm $inDir/runseeds.txt
+inDir=$(dirname "${1}")
+if [ -e "$inDir"/runseeds.txt ]; then
+   rm "$inDir"/runseeds.txt
 fi
 
-tr '\015' '\012' < ${1} > tmp_seedList.csv
+tr '\015' '\012' < "${1}" > tmp_seedList.csv
 
 awk -F, '{$1=$1"_"$x;for(i=1;i<=NF;i++)if(i!=x)f=f?f FS $i:$i;print f;f=""}' x=6 tmp_seedList.csv > tmp_seedList2.csv
 mv tmp_seedList2.csv tmp_seedList.csv
-for seed in $(awk -F","  'NR!=1{print $1}' tmp_seedList.csv); do
 
-echo $seed
-coord=$(awk -v var="$seed" -F"," '{if($1==var) print $2,$3,$4;}' tmp_seedList.csv)
+awk -F","  'NR!=1{print $1}' tmp_seedList.csv | while IFS= read -r seed; do
+    echo "$seed"
+    coord=$(awk -v var="$seed" -F"," '{if($1==var) print $2,$3,$4;}' tmp_seedList.csv)
 
-if [[ $2 == "" ]]; then
-   study=$(awk -v var="$seed" -F"," '{if($1==var) print $6;}' tmp_seedList.csv)
-else
-    study=${2}
-fi
+    if [[ $2 == "" ]]; then
+        study=$(awk -v var="$seed" -F"," '{if($1==var) print $6;}' tmp_seedList.csv)
+    else
+        study=${2}
+    fi
 
-size=$(awk -v var="$seed" -F"," '{if($1==var) print $5;}' tmp_seedList.csv)
+    size=$(awk -v var="$seed" -F"," '{if($1==var) print $5;}' tmp_seedList.csv)
 
-sh makeROI.sh $coord mm $size sphere ${study}_${seed}
+    sh makeROI.sh "$coord" mm "$size" sphere "${study}_${seed}"
 
 
-# txt file of newly made seeds that can be fed into seedVoxelCorrelation.sh
-echo ${study}_${seed} >> $inDir/runseeds.txt
+    # txt file of newly made seeds that can be fed into seedVoxelCorrelation.sh
+    echo "${study}_${seed}" >> "$inDir"/runseeds.txt
 done
 
 

motionScrub.sh

@@ -8,8 +8,8 @@
 #       c. 2=No Scrubbing, Motion Scrubbing in parallel
 ##################################################################################################################
 
-scriptPath=`perl -e 'use Cwd "abs_path";print abs_path(shift)' $0`
-scriptDir=`dirname $scriptPath`
+scriptPath=$(perl -e 'use Cwd "abs_path";print abs_path(shift)' "$0")
+scriptDir=$(dirname "$scriptPath")
 filename=run_motionscrub.m
 
 
@@ -24,44 +24,44 @@ function Usage {
 
 ########## FSL's arg parsing functions ###################
 get_opt1() {
-    arg=$(echo $1 | sed 's/=.*//')
-    echo $arg
+    arg=${1//=*/}
+    echo "$arg"
 }
 
 
 get_imarg1() {
-    arg=$(get_arg1 $1);
-    arg=$($FSLDIR/bin/remove_ext $arg);
-    echo $arg
+    arg=$(get_arg1 "$1");
+    arg=$("$FSLDIR"/bin/remove_ext "$arg");
+    echo "$arg"
 }
 
 get_arg1() {
-    if [ X"`echo $1 | grep '='`" = X ] ; then
+    if [ X"$(echo "$1" | grep '=')" = X ] ; then
 	echo "Option $1 requires an argument" 1>&2
 	exit 1
     else
-	arg=`echo $1 | sed 's/.*=//'`
-	if [ X$arg = X ] ; then
+	arg=${1//*=/}
+	if [ X"$arg" = X ] ; then
 	    echo "Option $1 requires an argument" 1>&2
 	    exit 1
 	fi
-	echo $arg
+	echo "$arg"
     fi
 }
 
 
 # Parse Command line arguments
 if [ $# -lt 1 ] ; then Usage; exit 0; fi
 while [ $# -ge 1 ] ; do
-    iarg=$(get_opt1 $1);
+    iarg=$(get_opt1 "$1");
     case "$iarg"
 	in
     --epi)
-  	    epiData=`get_arg1 $1`;
+  	    epiData=$(get_arg1 "$1");
         export epiData;
-        indir=$(dirname $epiData);
+        indir=$(dirname "$epiData");
         export indir;
-        rawEpiDir=$(dirname $(x=$indir; while [ "$x" != "/" ] ; do x=`dirname "$x"`; find "$x" -maxdepth 1 -type f -name "mcImg.nii.gz"; done 2>/dev/null));
+        rawEpiDir=$(dirname "$(x=$indir; while [ "$x" != "/" ] ; do x=$(dirname "$x"); find "$x" -maxdepth 1 -type f -name "mcImg.nii.gz"; done 2>/dev/null)");
         export rawEpiDir
         if [ "$epiData" == "" ]; then
           echo "Error: The restingStateImage (-E) is a required option"
@@ -80,29 +80,31 @@ done
 
 ##Echo out all input parameters into a log
 logDir=$rawEpiDir
-echo "$scriptPath" >> $logDir/rsParams_log
-echo "------------------------------------" >> $logDir/rsParams_log
-echo "-E $epiData" >> $logDir/rsParams_log
-echo "`date`" >> $logDir/rsParams_log
-echo "" >> $logDir/rsParams_log
-echo "" >> $logDir/rsParams_log
+{ 
+  echo "$scriptPath"
+  echo "------------------------------------"
+  echo "-E $epiData"
+  date
+  echo ""
+  echo ""
+} >> "$logDir"/rsParams_log
 
-cd $indir || exit
-gunzip ${epiData}
+cd "$indir" || exit
+gunzip "${epiData}"
 
 
 echo "Running $0 ..."
 
 
 
-cd $rawEpiDir || exit
+cd "$rawEpiDir" || exit
 
 
 # Extract image dimensions from the NIFTI File
-numXdim=`fslinfo $epiData | grep ^dim1 | awk '{print $2}'`
-numYdim=`fslinfo $epiData | grep ^dim2 | awk '{print $2}'`
-numZdim=`fslinfo $epiData | grep ^dim3 | awk '{print $2}'`
-numtimepoint=`fslinfo $epiData | grep ^dim4 | awk '{print $2}'`
+numXdim=$(fslinfo "$epiData" | grep ^dim1 | awk '{print $2}')
+numYdim=$(fslinfo "$epiData" | grep ^dim2 | awk '{print $2}')
+numZdim=$(fslinfo "$epiData" | grep ^dim3 | awk '{print $2}')
+numtimepoint=$(fslinfo "$epiData" | grep ^dim4 | awk '{print $2}')
 
 
 
@@ -123,17 +125,17 @@ EOF
 
 
 # Run script using Matlab or Octave
-haveMatlab=`which matlab`
+haveMatlab=$(which matlab)
 if [ "$haveMatlab" == "" ]; then
-  octave --no-window-system $rawEpiDir/$filename
+  octave --no-window-system "$rawEpiDir/$filename"
 else
   matlab -nodisplay -r "run $rawEpiDir/$filename"
 fi
 
 #################################
 
 
-cd ${rawEpiDir}/motionScrub || exit
+cd "${rawEpiDir}"/motionScrub || exit
 #### Process Summary ############
 echo "...Summarizing Results"
 
@@ -144,34 +146,35 @@ fsl_tsplot -i fd.txt -t "FD (mm)" -w 800 -h 300 -u 1 --start=1 -o fd.png
 fsl_tsplot -i dvars.txt -t "DVARS" -w 800 -h 300 -u 1 --start=1 -o dvars.png
 ##Echo out the pertinent info for the motion-scrubbed/processed subjects
 
-numvols=`fslinfo ${epiData} | grep ^dim4 | awk '{print $2}'`
+numvols=$(fslinfo "${epiData}" | grep ^dim4 | awk '{print $2}')
 
-delvols=`cat deleted_vols.txt | wc | awk '{print $2}'`
+delvols=$(wc < deleted_vols.txt | awk '{print $2}')
 
-propdel=`echo ${numvols} ${delvols} | awk '{print ($2/$1)}'`
-residvols=`echo ${numvols} ${delvols} | awk '{print ($1-$2)}'`
+propdel=$(echo "${numvols} ${delvols}" | awk '{print ($2/$1)}')
+residvols=$(echo "${numvols} ${delvols}" | awk '{print ($1-$2)}')
 echo "${indir},${numvols},${delvols},${propdel},${residvols}" >> motion_scrubbing_info.txt
 
 #Echo out motionscrub info to rsParams file
-echo "epiNormMS=${epiData//.nii/_ms.nii}" >> $rawEpiDir/rsParams
+echo "epiNormMS=${epiData//.nii/_ms.nii}" >> "$rawEpiDir"/rsParams
 
 
+{
+  echo "<hr>"
+  echo "<h2>Motion Scrubbing</h2>"
+  echo "<b>Total Volumes</b>: $numvols<br>"
+  echo "<b>Deleted Volumes</b>: $delvols<br>"
+  echo "<b>Remaining Volumes</b>: $residvols<br>"
+ } >> "${rawEpiDir}"/analysisResults.html
 
-echo "<hr>" >> ${rawEpiDir}/analysisResults.html
-echo "<h2>Motion Scrubbing</h2>" >> ${rawEpiDir}/analysisResults.html
-echo "<b>Total Volumes</b>: $numvols<br>" >> ${rawEpiDir}/analysisResults.html
-echo "<b>Deleted Volumes</b>: $delvols<br>" >> ${rawEpiDir}/analysisResults.html
-echo "<b>Remaining Volumes</b>: $residvols<br>" >> ${rawEpiDir}/analysisResults.html
 
-
-scrubDataCheck=`cat deleted_vols.txt | head -1`
+scrubDataCheck=$(head -1 deleted_vols.txt)
 if [[ $scrubDataCheck != "" ]]; then
-  echo "<b>Scrubbed TR</b>: `cat deleted_vols.txt | awk '{$1=$1}1'`<br>" >> ${rawEpiDir}/analysisResults.html
+  echo "<b>Scrubbed TR</b>: $(awk '{$1=$1}1' deleted_vols.txt)<br>" >> "${rawEpiDir}"/analysisResults.html
 fi
 
 #################################
 # clean up gunzipped nifti
-gzip ${epiData//.nii.gz/.nii}
+gzip "${epiData//.nii.gz/.nii}"
 
 echo "$0 Complete"
 echo ""

proc_fmap.sh

@@ -4,10 +4,10 @@
 inFile=$1
 
 #Adjust the fieldMap_Hz to rad/s by multiplying by 6.28 (2*pi=6.28)
-fslmaths ${inFile} -mul 6.28 ${inFile}
+fslmaths "${inFile}" -mul 6.28 "${inFile}"
 
 # https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide#Step_5_-_Regularising_the_fieldmap
 # smooth (1mm), despike, median filter
-fugue --loadfmap=${inFile} -s 1 --savefmap=${inFile%.nii.gz}_prepped.nii.gz
-fugue --loadfmap=${inFile} --despike --savefmap=${inFile%.nii.gz}_prepped.nii.gz
-fugue --loadfmap=${inFile} -m --savefmap=${inFile%.nii.gz}_prepped.nii.gz
+fugue --loadfmap="${inFile}" -s 1 --savefmap="${inFile%.nii.gz}"_prepped.nii.gz
+fugue --loadfmap="${inFile}" --despike --savefmap="${inFile%.nii.gz}"_prepped.nii.gz
+fugue --loadfmap="${inFile}" -m --savefmap="${inFile%.nii.gz}"_prepped.nii.gz