lnifmri_prep05_qc

#!/bin/bash
#
# LNiF MRI Lab Pipeline for preprocessing of
# structural and functional MRI dataset
# stefano.tambalo@unitn.it - 20200310
# rev. 20210513
#
# Generation of utility files and report for visual QC
#
########################################################################
export LC_ALL=C

shopt -s extglob

UsageFSL() {
    printf "\n***************************************************\n"
    printf "LNiF MRI Lab Preprocessing Pipeline\n"
    printf "CIMeC - Center for Mind/Brain Science\n\n"
    printf "\tFSLDIR not set!\n\n"
    printf "\tRequires:\n\t\tFSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL)\n"
    printf "\n\n(c) stefano.tambalo@unitn.it, 2020.\n"
    printf "***************************************************\n\n"
    exit 1
}

Start() {
    stamp=`date +%Y%m%d_%H%M%S`	
    printf "\n***************************************************\n"
    printf "LNiF MRI Lab Preprocessing Pipeline\n"
    printf "CIMeC - Center for Mind/Brain Science\n\n"
    printf "Building QC summary\n"        
}

NextStep() {
    printf "Complete. Exec. Time: ${exectime}\n\n"
	printf "To browse a QC summary of your data, open:\n"    
	printf "file: %s\n" "./lnifmri_prep_report.html"    	
    printf "\n\n***************************************************\n\n"
    exit 1
}

[ "$FSLDIR" = "" ] && UsageFSL
exectime=0
SECONDS=0
QCDIR=./qc
LOGDIR=./logs

stamp=`date +%Y%m%d_%H%M%S`

Start

###############################################################################################	
# MOTION Section
###############################################################################################	

###############################################################################################
# Compose summary motion report
pnglist=""
for epiimg in `cat ${LOGDIR}/lnifmri_prep_inputlist.txt` ; do

    epiname=$($FSLDIR/bin/remove_ext ${epiimg})
    
    readarray -d / -t fileparts <<< "${epiimg}"
    sid=$((${#fileparts[@]}-3))
    subID=$(echo ${fileparts[${sid}]})

	# Compose a single-subject motion report
	rot=${epiname}_rot.png
	tra=${epiname}_tra.png
	mot=${epiname}_motout.png
	# Link 3 motion charts in a single row
	printf -v str  "%s + %s + %s" "$mot" "$rot" "$tra" 
	[[ -z "$pnglist" ]] && pnglist="${pnglist} ${str}" || pnglist="${pnglist} - ${str}"
done

# Create final plot
$FSLDIR/bin/pngappend ${pnglist} ${QCDIR}/lnifmri_prep_qc_motion.png

###############################################################################################
# Create final boxplot with RMS displacement for each scan
paste -d " " $(ls -d1 ./sub*/func/*abs.rms | cat) > ${QCDIR}/qc_report_rmsabs_boxplot_full.txt
# Trim unequal lenght
maxcol=$(awk '{print NF}' ${QCDIR}/qc_report_rmsabs_boxplot_full.txt | sort -nu | tail -n 1)
awk -v var=${maxcol} 'NF==var' ${QCDIR}/qc_report_rmsabs_boxplot_full.txt > ${QCDIR}/qc_report_rmsabs_boxplot.txt
numrow=$(awk '{print NR}' ${QCDIR}/qc_report_rmsabs_boxplot.txt | tail -n 1)
printf "\n\tRMS Abs. Disp.: trimming RMS data to ${numrow} volumes.\n"

printf "\tMAXCOL\t${maxcol}\n\tNUMROW\t${numrow}\n"

$FSLDIR/bin/fsl_boxplot	-i ${QCDIR}/qc_report_rmsabs_boxplot.txt \
						--title="Abs. Displ. (mm)" \
						--ylabel="Abs. RMS (mm)" \
						--xlabel="Scan Code" \
						-o ${QCDIR}/qc_report_rmsabs_boxplot.png;

paste -d " " $(ls -d1 ./sub*/func/*rel.rms | cat) > ${QCDIR}/qc_report_rmsrel_boxplot_full.txt
# Trim unequal lenght
maxcol=$(awk '{print NF}' ${QCDIR}/qc_report_rmsrel_boxplot_full.txt | sort -nu | tail -n 1)
awk -v var=${maxcol} 'NF==var' ${QCDIR}/qc_report_rmsrel_boxplot_full.txt > ${QCDIR}/qc_report_rmsrel_boxplot.txt
numrow=$(awk '{print NR}' ${QCDIR}/qc_report_rmsrel_boxplot.txt | tail -n 1)
printf "\n\tRMS Rel. Disp.: trimming RMS data to ${numrow} volumes.\n"

printf "\tMAXCOL\t${maxcol}\n\tNUMROW\t${numrow}\n"

$FSLDIR/bin/fsl_boxplot	-i ${QCDIR}/qc_report_rmsrel_boxplot.txt \
						--title="Rel. Displ. (mm)" \
						--ylabel="Rel. RMS (mm)" \
						--xlabel="Scan Code" \
						-o ${QCDIR}/qc_report_rmsrel_boxplot.png;

$FSLDIR/bin/pngappend ${QCDIR}/qc_report_rmsabs_boxplot.png + ${QCDIR}/qc_report_rmsrel_boxplot.png ${QCDIR}/lnifmri_prep_qc_motion_rms.png

# Compose table headers for motion RMS data table
printf "%s\t%s\t%s\t%s\t%s\t%s\n" "SubID" "SesID" "aRMS(mm)" "rRMS(mm)" "nOut" 'pOut(%)'> ${QCDIR}/qc_motion_rms_table_header.txt
# Final rendering of motion RMS data table
cat ${QCDIR}/qc_motion_rms_table_header.txt ${QCDIR}/qc_motion_rms_table.txt | sed 's/\t/,|,/g' | column -s ',' -t > ${QCDIR}/lnifmri_prep_qc_report_motion_rms.txt

###############################################################################################
# Compose common table headers for descriptive stats data
printf "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" "SubID" "SesID" "Par" "#Vol" "Sum" "Avg" "Med" "StD" "min" "MAX" > ${QCDIR}/qc_report_motion_dstats_header.txt

# Here consider only full data (X, Y, Z)
printf "%s\n%s\n%s\n%s\n%s\n%s\n" "Rot X(rad)" "Rot Y(rad)" "Rot Z(rad)" "Tra X(mm)" "Tra Y(mm)" "Tra Z(mm)" > ${QCDIR}/qc_report_motion_dstats_full_par.txt
for d in `ls -d1 ${QCDIR}/qc_motion_*_dstats_full.txt`; do
	paste -d "\t" ${d%.txt}_subseskey.txt ${QCDIR}/qc_report_motion_dstats_full_par.txt ${d} >> ${QCDIR}/qc_report_motion_dstats_full_temp.txt
done
cat ${QCDIR}/qc_report_motion_dstats_header.txt ${QCDIR}/qc_report_motion_dstats_full_temp.txt > ${QCDIR}/qc_report_motion_dstats_full.txt
# Final rendering of dstats
cat ${QCDIR}/qc_report_motion_dstats_full.txt | sed 's/\t/,|,/g' | column -s ',' -t > ${QCDIR}/lnifmri_prep_qc_report_motion_dstats_full.txt

# Here consider only compact data (X, Y, Z)
printf "%s\n%s\n" "AvgRot XYZ (rad)" "AvgTra XYZ (mm)" > ${QCDIR}/qc_report_motion_dstats_compact_par.txt
for d in `ls -d1 ${QCDIR}/qc_motion_*_dstats_compact.txt`; do
	paste -d "\t" ${d%.txt}_subseskey.txt ${QCDIR}/qc_report_motion_dstats_compact_par.txt ${d} >> ${QCDIR}/qc_report_motion_dstats_compact_temp.txt
done
cat ${QCDIR}/qc_report_motion_dstats_header.txt ${QCDIR}/qc_report_motion_dstats_compact_temp.txt > ${QCDIR}/qc_report_motion_dstats_compact.txt
# Final rendering of dstats
cat ${QCDIR}/qc_report_motion_dstats_compact.txt | sed 's/\t/,|,/g' | column -s ',' -t > ${QCDIR}/lnifmri_prep_qc_report_motion_dstats_compact.txt

###############################################################################################
# Compose summary SNR/tSNR report

ls -d1 ./sub*/func/*tSNR.nii.gz     > ${QCDIR}/qc_report_tSNRbas_list.txt
ls -d1 ./sub*/func/sdc_unc/*tSNR.nii.gz > ${QCDIR}/qc_report_tSNRunc_list.txt

printf "raw\nunc" > ${QCDIR}/qc_report_tSNR_boxplotlegend.txt

# Combine all tSNR maps in a lightbox view
pnglist=""
for epiimg in `cat ${QCDIR}/qc_report_tSNRbas_list.txt` ; do

    epiname=$($FSLDIR/bin/remove_ext ${epiimg})    
    readarray -d / -t fileparts <<< "${epiimg}"
    sid=$((${#fileparts[@]}-3))
    subID=$(echo ${fileparts[${sid}]})

    # For boxplot chart
    $FSLDIR/bin/fslstats ${epiimg} -n -M >> ${QCDIR}/qc_report_tSNRbas_boxplot.txt

		# min value of tSNR (to scale lightbox colorbars)
		mR=$($FSLDIR/bin/fslstats ${epiimg} -n -r | awk '{print $1}')
		# max value of tSNR (to scale lightbox colorbars)
		MR=$($FSLDIR/bin/fslstats ${epiimg} -n -r | awk '{print $2}')

    # For lightbox image
    str="${QCDIR}/qc_report_tSNRbas_${subID}.png"
    $FSLDIR/bin/fsleyes render  --scene lightbox -ss 3 -hc -hl \
																-cb -cbl right -ls 9 -cbi 50 \
    	                        	--outfile ${str} \
            	                	${epiimg} -dr ${mR} ${MR} -cm greyscale;
   	
    [[ -z "$pnglist" ]] && pnglist="${pnglist} ${str}" || pnglist="${pnglist} - ${str}"
done
$FSLDIR/bin/pngappend ${pnglist} ${QCDIR}/qc_report_tSNRbas.png

pnglist=""
for epiimg in `cat ${QCDIR}/qc_report_tSNRunc_list.txt` ; do
	
    epiname=$($FSLDIR/bin/remove_ext ${epiimg})
    readarray -d / -t fileparts <<< "${epiimg}"
    sid=$((${#fileparts[@]}-4))
    subID=$(echo ${fileparts[${sid}]})

    # For boxplot chart
    $FSLDIR/bin/fslstats -t ${epiimg} -n -M >> ${QCDIR}/qc_report_tSNRunc_boxplot.txt

		# min value of tSNR (to scale lightbox colorbars)
		mR=$($FSLDIR/bin/fslstats ${epiimg} -n -r | awk '{print $1}')
		# max value of tSNR (to scale lightbox colorbars)
		MR=$($FSLDIR/bin/fslstats ${epiimg} -n -r | awk '{print $2}')

    # For lightbox image
    str="${QCDIR}/qc_report_tSNRunc_${subID}.png"
    $FSLDIR/bin/fsleyes render  --scene lightbox -ss 3 -hc -hl \
    							-cb -cbl right -ls 9 -cbi 50 \
    							--outfile ${str} \
    							${epiimg} -dr ${mR} ${MR} -cm greyscale;

    [[ -z "$pnglist" ]] && pnglist="${pnglist} ${str}" || pnglist="${pnglist} - ${str}"
done
$FSLDIR/bin/pngappend ${pnglist} ${QCDIR}/qc_report_tSNRunc.png

$FSLDIR/bin/pngappend ${QCDIR}/qc_report_tSNRbas.png + ${QCDIR}/qc_report_tSNRunc.png ${QCDIR}/lnifmri_prep_qc_tSNR_lightbox.png

# Combine all values in a n-column file for boxplot
paste -d " " $(ls -d1 ${QCDIR}/qc_report_tSNR*boxplot.txt) > ${QCDIR}/qc_report_tSNR_boxplot.txt
$FSLDIR/bin/fsl_boxplot	-i ${QCDIR}/qc_report_tSNR_boxplot.txt \
						--title="temporal SNR" \
						--ylabel="tSNR (a.u.)" \
						--xlabel="Scan Type" \
						--legend=${QCDIR}/qc_report_tSNR_boxplotlegend.txt \
						--height=220 \
						-o ${QCDIR}/lnifmri_prep_qc_tSNR_boxplot.png;

###############################################################################################	
# POWER SPECTRUM Section
###############################################################################################	

###############################################################################################
# Compose summary power spectra report

for subID in `cat ${QCDIR}/qc_screen_subs_uniq.txt` ; do
	plots=$(ls -d1 ${subID}/func/sdc_unc/*_spectra.txt)
	pslist=""
	# In case there is only TASK data	
	if [ -z "$plots" ]; then
		printf "${subID}: Power spectra not found!\n"		
	else
		# Load subj specific plot data
		for p in ${plots}; do
			path=$(dirname ${p})
			id=${p%.txt}
			printf -v plotDATAID "${id}%s" "specs.txt"
			readarray -t plotDATA < "${plotDATAID}"
			# echo ${plotDATA[@]}
			ps="${path}/${plotDATA[1]}_${plotDATA[2]}_spectra.png"
			$FSLDIR/bin/fsl_tsplot	-i ${p} \
									-u ${plotDATA[0]} \
									-y "Power" -x "Frequency (Hz)" \
									-t "${plotDATA[1]}_${plotDATA[2]} - GMw Power Spectrum - TR(s): ${plotDATA[3]}" \
									-a raw,bpf -w 660 -h 220 \
									--start=1 --finish=2 \
									-o ${ps};
			# printf "${subID}: ${ps}\n"		
	   		[[ -z "$pslist" ]] && pslist="${pslist} ${ps}" || pslist="${pslist} + ${ps}"
   		done
	fi
 	$FSLDIR/bin/pngappend ${pslist} ${QCDIR}/qc_report_pspec_${subID}.png
done

#Create final plot (power spectrum)
printf -v pspeclist "$( ls -d1 ${QCDIR}/qc_report_pspec_sub*.png | sed ':a;N;$!ba;s/\n/ - /g' )"
$FSLDIR/bin/pngappend ${pspeclist} $QCDIR/lnifmri_prep_qc_pspec.png

###############################################################################################	
# SDC Section
###############################################################################################	

###############################################################################################
# Compose summary SDC methods available for subID
# Update labels in case some options are missing (FMP, TUP or both)

for subID in `cat ${QCDIR}/qc_screen_subs_uniq.txt` ; do
	fs="fmp,"
	ts="tup,"
	us="unc"

	if [ ! -d ${subID}/func/sdc_fmp ]; then
		fs="---,"
	fi
	if [ ! -d ${subID}/func/sdc_tup ]; then
		ts="---,"
	fi
	printf "(Avail. SDC: %s)\n" "${fs}${ts}${us}" >> ${QCDIR}/qc_report_sdc.txt
done #for subID

###############################################################################################	
# Filelist Section
###############################################################################################	

###############################################################################################
# Create filelist for group-ICA in MNI space
# if 	[ -e ./sub*/func/sdc_fmp/*MNI-smooth.nii.gz ]; then
	ls -d1 ./sub*/func/sdc_fmp/*MNI-smooth.nii.gz > filelist_groupICA_fmp.txt
# else
# 	printf "\n\tFieldmap SDC data not available.\n"
# fi

# if 	[ -e ./sub*/func/sdc_tup/*MNI-smooth.nii.gz ]; then
	ls -d1 ./sub*/func/sdc_tup/*MNI-smooth.nii.gz > filelist_groupICA_tup.txt
# else
# 	printf "\n\tAP/PA SDC data not available.\n"	
# fi

ls -d1 ./sub*/func/sdc_unc/*MNI-smooth.nii.gz > filelist_groupICA_unc.txt

###############################################################################################
# Create filelist for motion parameters files in subject space

ls -d1 ./sub*/func/*.par > ${QCDIR}/filelist_motionparameters.txt
ls -d1 ./sub*/func/*motoutplot.txt > ${QCDIR}/filelist_motiondvars.txt

###############################################################################################	
# HTML Section
###############################################################################################	

printf "\nCreating HTML report\n\n"	

###############################################################################################
# Create some utility files for the HTML report

cp ${QCDIR}/qc_screen_keyheaders.txt 		  ${QCDIR}/lnifmri_prep_qc_report_keyheaders.txt
cp ${QCDIR}/qc_screen_formattedtable.txt 	${QCDIR}/lnifmri_prep_qc_report_formattedtable.txt
cp ${QCDIR}/qc_screen_purgedscans.txt 		${QCDIR}/lnifmri_prep_qc_report_purgedscans.txt

# Input list with SDC info
paste -d " " ${QCDIR}/qc_screen_subs_uniq.txt ${QCDIR}/qc_report_sdc.txt > ${QCDIR}/lnifmri_prep_qc_report_subssdc.txt

# Conversion list raw subj-name -> sub-XX
printf "%s ->\n" `ls -d1 ../*.sub` > ${QCDIR}/qc_screen_rawsubs.txt
paste ${QCDIR}/qc_screen_rawsubs.txt ${QCDIR}/qc_screen_subs_uniq.txt > ${QCDIR}/lnifmri_prep_qc_report_rawtosubs.txt

# List to populate registration gallery to std
ls -d1 ${QCDIR}/lnifmri_prep_func2std_QC/*sub-*.png > ${QCDIR}/qc_report_regtostd_images.txt
for s in `cat ${QCDIR}/qc_report_regtostd_images.txt`; do
	case "${s}" in
		*fmap*)
			printf "%s(fmp)\n" `grep -oP "sub-[0-9][0-9]" <<< ${s}` >>  ${QCDIR}/qc_report_regtostd_captions.txt
		;;
		*tup*)
			printf "%s(tup)\n" `grep -oP "sub-[0-9][0-9]" <<< ${s}` >>  ${QCDIR}/qc_report_regtostd_captions.txt
		;;
		*unc*)
			printf "%s(unc)\n" `grep -oP "sub-[0-9][0-9]" <<< ${s}` >>  ${QCDIR}/qc_report_regtostd_captions.txt
		;;
	esac
done
paste -d "|" ${QCDIR}/qc_report_regtostd_images.txt ${QCDIR}/qc_report_regtostd_captions.txt > ${QCDIR}/qc_report_regtostd_media.txt
awk	-F \| '
	{printf "<div class=\"container\">\n\t<img src=\"%s\" alt=\"Reg2Std\" class=\"responsive\">\n\t<div class=\"top-left\">%s</div>\n</div>\n", $1, $2}' \
	${QCDIR}/qc_report_regtostd_media.txt > ${QCDIR}/lnifmri_prep_qc_report_regtostd.txt

# List to populate registration gallery to struc 
ls -d1 ${QCDIR}/lnifmri_prep_func2struc_QC/*sub-*.png > ${QCDIR}/qc_report_regtostruc_images.txt
for s in `cat ${QCDIR}/qc_report_regtostruc_images.txt`; do
	case "${s}" in
		*fmap*)
			printf "%s(fmp)\n" `grep -oP -m 1 "sub-[0-9][0-9]" <<< ${s}` >>  ${QCDIR}/qc_report_regtostruc_captions_temp.txt
		;;
		*tup*)
			printf "%s(tup)\n" `grep -oP -m 1 "sub-[0-9][0-9]" <<< ${s}` >>  ${QCDIR}/qc_report_regtostruc_captions_temp.txt
		;;
		*unc*)
			printf "%s(unc)\n" `grep -oP -m 1 "sub-[0-9][0-9]" <<< ${s}` >>  ${QCDIR}/qc_report_regtostruc_captions_temp.txt
		;;
	esac
done
uniq ${QCDIR}/qc_report_regtostruc_captions_temp.txt > ${QCDIR}/qc_report_regtostruc_captions.txt
paste -d "|" ${QCDIR}/qc_report_regtostruc_images.txt ${QCDIR}/qc_report_regtostruc_captions.txt > ${QCDIR}/qc_report_regtostruc_media.txt
awk	-F \| '
	{printf "<div class=\"container\">\n\t<img src=\"%s\" alt=\"Reg2Std\" class=\"responsive\">\n\t<div class=\"top-left\">%s</div>\n</div>\n", $1, $2}' \
	${QCDIR}/qc_report_regtostruc_media.txt > ${QCDIR}/lnifmri_prep_qc_report_regtostruc.txt

###############################################################################################
# Create an HTML report
cat << EOR > lnifmri_prep_report.html
<!DOCTYPE html>
<html>
<head>
<meta name="viewport" content="width=device-width, initial-scale=1">
<style>
* {box-sizing: border-box}

body, html {
  height: 100%;
  margin: 0;
  font-family: "Courier New", Courier, monospace;
}

.header {
  padding: 20px;
  text-align: center;
  background: #555;
  color: white;
  font-size: 24px;
}

img {
  display: block;
  margin-left: auto;
  margin-right: auto;
  width: 50%;
}

#navbar {
  overflow: hidden;
  background-color: #555;
}

.sticky {
  position: fixed;
  top: 0;
  width: 100%;
}

.content {
  padding: 16px;
}

.sticky + .content {
  padding-top: 60px;
}

.tablink {
  background-color: #555;
  color: white;
  float: left;
  border: none;
  outline: none;
  cursor: pointer;
  padding: 14px 16px;
  font-size: 18px;
  width: 16.66%;
  display: table-cell;
}

.tablink:hover {
  background-color: #777;
}

.tabcontent {
  color: black;
  display: none;
  padding: 20px 20px;
  padding-top: 50px;
  height: 100%;
}

.responsive {
	width: 100%;
	height: auto;
}

.footer {
  position: fixed;
  left: 0;
  bottom: 0;
  width: 100%;
  background-color: #555;
  color: white;
  text-align: center;
}

.column {
  float: left;
  width: 50%;
  padding: 25px 100px 50px;
  margin: auto;
}

.row:after {
  content: "";
  display: table;
  clear: both;
}

@media screen and (max-width: 600px) {
  .column {
    width: 100%;
  }

.container {
  display: flex;
  flex-wrap: wrap;
  padding: 0 4px;
  position: relative;
  text-align: center;
  color: white;
  background-color: white;

}

/* Top left text */
.top-left {
  position: absolute;
  top: 8px;
  left: 16px;
}

/* Solid border */
hr.solid {
  border-top: 3px solid #555;
}

</style>
</head>
<body>

<div class="header">
  <h1>lnifmri_prep</h1>
  <p>Quality Control Report</p>
</div>

<div id="navbar">
<button class="tablink" onclick="openPage('GEN', this, 'white')" id="defaultOpen">GENERAL</button>
<!--
####################################################################### HIDDEN BUTTON
<button class="tablink" onclick="openPage('ACQ', this, 'white')">ACQP</button>
################################################################ END OF HIDDEN BUTTON
-->
<button class="tablink" onclick="openPage('MNI', this, 'white')">MNI</button>
<button class="tablink" onclick="openPage('T1w', this, 'white')">T1w</button>
<button class="tablink" onclick="openPage('MOT', this, 'white')">MOTCO</button>
<button class="tablink" onclick="openPage('PWR', this, 'white')">PWR</button>
<button class="tablink" onclick="openPage('tSNR', this, 'white')">tSNR</button>
</div>

<!--
<hr class="solid">
-->

<div id="GEN" class="tabcontent">
<br>
  <p style="text-align: center;"><b>Output dir</b>: $(pwd)</p>
 <br>
 <div class="row">
 	<div class="column">
  		<h2>List of Available Subjects:</h2>
  		<pre>$(cat ${QCDIR}/lnifmri_prep_qc_report_rawtosubs.txt)</pre>
	</div>
  	<div class="column">
  		<h2>List of Processed Subjects:</h2>
  		<pre>$(cat ${QCDIR}/lnifmri_prep_qc_report_subssdc.txt)</pre>
	</div>
 </div>
 <div class="row">
  	<div class="column">
  		<h2>Summary of Acq. Parameters:</h2>
  		<pre>$(cat ${QCDIR}/lnifmri_prep_qc_report_keyheaders.txt)</pre>
  		<pre>$(cat ${QCDIR}/lnifmri_prep_qc_report_formattedtable.txt)</pre>
	</div>
  	<div class="column">
  		<h2>List of Excluded Scans (Code):</h2>
  		<pre>$(cat ${QCDIR}/lnifmri_prep_qc_report_purgedscans.txt)</pre>
	</div>
</div>
 <div class="row">
  	<div class="column">
  		<h2>tSNR (RAW vs. SDC-unc.)</h2>
		<img src="${QCDIR}/lnifmri_prep_qc_tSNR_boxplot.png" alt="tSNR">
	</div>
	<div class="column">
  		<h2>Summary of RAW motion data</h2>
		<pre>$(cat ${QCDIR}/lnifmri_prep_qc_report_motion_rms.txt)</pre>
	</div>
</div>
<br><br><br><br>
</div>

<!--
############################################################################ HIDDEN TAB
<div id="ACQ" class="tabcontent">
  <h3 style="text-align: center";>Acquisition Parameters</h3>
  <p style="text-align: center";></p>
<br><br><br>
  <img src="${QCDIR}/lnifmri_prep_qc_acqpars.png" alt="ACQPars - Data Not Available">
<br><br><br><br>
</div>
##################################################################### END OF HIDDEN TAB
--> 

<div id="MOT" class="tabcontent">
  <h3 style="text-align: center";>Estimated mean displacement</h3>
<br><br><br>
  <img src="${QCDIR}/lnifmri_prep_qc_motion_rms.png" alt="RMSPars" class="responsive">
<br><br><br>
  <h3 style="text-align: center";>Estimation of Motion</h3>
  <p style="text-align: center";>Motion Outliers, In-plane translations and rotations</p>
<br><br><br>
  <img src="${QCDIR}/lnifmri_prep_qc_motion.png" alt="MOTPars" class="responsive">
<br><br><br><br>
</div>

<div id="MNI" class="tabcontent">
  <h3 style="text-align: center";>Registration to MNI brain template</h3>
  <p style="text-align: center";>Functional EPI to Standard Space Template</p>
<br><br><br>
  $(cat ${QCDIR}/lnifmri_prep_qc_report_regtostd.txt)
<br><br><br><br>
</div>

<div id="T1w" class="tabcontent">
  <h3 style="text-align: center";>Registration to T1w</h3>
  <p style="text-align: center";>Functional EPI to Subject Space Anatomical Scan</p>
<br><br><br>
  $(cat ${QCDIR}/lnifmri_prep_qc_report_regtostruc.txt)
<br><br><br><br>
</div>

<div id="PWR" class="tabcontent">
  <h3 style="text-align: center";>Power Spectrum of Timeseries</h3>
  <p style="text-align: center";>Overlay of raw and BPF, SD-uncorrected timeseries</p>
<br><br><br>
  <img src="${QCDIR}/lnifmri_prep_qc_pspec.png" alt="PSPECdata" class="responsive">
<br><br><br><br>
</div>

<div id="tSNR" class="tabcontent">
  <h3 style="text-align: center";>temporal SNR of Timeseries</h3>
  <p style="text-align: center";>Raw and Preprocessed, SD-uncorrected timeseries</p>
<br><br><br>
  <img src="${QCDIR}/lnifmri_prep_qc_tSNR_lightbox.png" alt="tSNR" class="responsive">
<br><br><br><br>
</div>

<div class="footer">
  <p>LNiF MRI Lab @ CIMeC, UniTN - Via delle Regole 101, Mattarello (TN); <i>Creation date</i>: ${stamp}</p>
</div>

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EOR

###############################################################################################	
# Clean up Section
###############################################################################################	

# # Clean up QC folder
# mkdir -p $QCDIR/lnifmri_prep_qcfiles
# mv $QCDIR/qc_*.txt $QCDIR/lnifmri_prep_qcfiles/
# mv $QCDIR/qc_*.png $QCDIR/lnifmri_prep_qcfiles/

# # Clean up subID folders 
# for sID in `cat ${QCDIR}/lnifmri_prep_qcfiles/qc_screen_subs_uniq.txt`; do
# 	mkdir -p ${sID}/func/lnifmri_prep_files
# 	ls -d1 ${sID}/func/*.* > ${sID}/func/${sID}_filelist.txt
# 	xargs mv -t ${sID}/func/lnifmri_prep_files/ < ${sID}/func/${sID}_filelist.txt
# done

duration=$SECONDS
printf -v exectime "$(($duration / 60))m:$(($duration % 60))s."
NextStep