Opciones de XNAT CLI para el QC de Freesurfer

Para obtener los archivos necesarios de XNAT, guardar y consultar los resultados hemos hecho extensiones de xnatapic.

Bajar directorios de FS

#!/bin/bash
 
ARGS=( "$@" )
HELP="prepare_fsqc - create the structure for Fresurfer QC with visualQC"
 
#local variables
PROJ_ID=""
OUTPUT_DIR=""
 
#global variables
[ -s "$XNATAPIC_APPS/xnat.conf" ] && . "$XNATAPIC_APPS/xnat.conf"
[ -s "$XNATAPIC_HOME_APPS/xnat.conf" ] && . "$XNATAPIC_HOME_APPS/xnat.conf"
 
#parse arguments
for ((n=0; n<${#ARGS[@]}; n++)) ; do
	case "${ARGS[$n]}" in
		--help-short)
			echo "$HELP"
			exit 0
			;;
		--help)
			echo "$HELP"
			cat <<.EOF
 --help: show this help
 --project <project id> [mandatory]
 --outdir <output directory> [defaults to <project id>_fsresults]
 --list <list of downloaded experiments> [defaults to <project id>_experiments.list]
.EOF
			exit 0
			;;
		--project)
			let n=n+1
			PROJ_ID="${ARGS[$n]}"
			;;
		--outdir)
			let n=n+1
			OUTPUT_DIR="$(echo "${ARGS[$n]}" | sed 's/[ \n\r\t]\+/+/g')"
			;;
		--list)
			let n=n+1
			OUTPUT_LIST="$(echo "${ARGS[$n]}" | sed 's/[ \n\r\t]\+/+/g')"
			;;	
		-*)
			echo "Warning: ignoring option or command ${ARGS[$n]}" >&2
			;;
		*)
			echo "Warning: ignoring option or command ${ARGS[$n]}" >&2
			;;
	esac
done
 
#checks
if [ -z "$PROJ_ID" ]; then
	echo "Error: a project ID is required" >&2
	exit 1
fi
#defaults
[ -z "$OUTPUT_DIR" ] && OUTPUT_DIR="${PROJ_ID}_fsresults"
[ -z "$OUTPUT_LIST" ] && OUTPUT_LIST="${PROJ_ID}_experiments.list"
#prepare
[ ! -d $OUTPUT_DIR ] && mkdir $OUTPUT_DIR
if [ -f $OUTPUT_LIST ]; then rm -rf $OUTPUT_LIST; fi
TEMP_ELIST=$(mktemp -t fsqc.XXXXXXXX)
#run
if ! curl -f -X GET -u "$USER:$PASSWORD" "$HOST/data/projects/$PROJ_ID/experiments?xsiType=xnat:mrSessionData" 2>/dev/null | jq '.' > $TEMP_ELIST ; then
	echo "Error: server reported an error" >&2
	exit 1;
else
	TOTAL=$(cat $TEMP_ELIST | jq '.ResultSet.totalRecords' | sed 's/"//g')
	let TOTAL=TOTAL-1
	for SBJ in $(seq 0 $TOTAL); do 
		XEXP=$(cat $TEMP_ELIST | jq ".ResultSet.Result[$SBJ].ID" | sed 's/"//g')
		echo "Processing $XEXP ... ($(($SBJ+1))/$(($TOTAL+1)))"
		FSR=`curl -f -X GET -u "$USER:$PASSWORD" "$HOST/data/experiments/$XEXP/files" 2>/dev/null | jq '.ResultSet.Result[].URI' | grep "\.tar\.gz" | sed 's/"//g'`
		if [ $FSR ]; then
			echo "$XEXP" >> $OUTPUT_LIST
			[ ! -d $OUTPUT_DIR/$XEXP ] && mkdir $OUTPUT_DIR/$XEXP
			TEMP_TAR=$(mktemp -t fsdir.XXXXXXXX.tar.gz)
			curl -f -X GET -u "$USER:$PASSWORD" "$HOST$FSR" -o $TEMP_TAR 2>/dev/null
			#tar xzf $TEMP_TAR --strip-components=1 -C $OUTPUT_DIR/$XEXP
			tar xzf $TEMP_TAR --strip-components=1 -C $OUTPUT_DIR/$XEXP */mri/{orig,aparc+aseg}.mgz */label/*.aparc.* */surf/*.pial
			rm $TEMP_TAR
		fi
	done	
fi
rm $TEMP_ELIST
echo "So long, and thanks for all the fish!"

Subir QC de FS

upload_fsqc

upload_fsqc.sh

#!/bin/bash
 
ARGS=( "$@" )
HELP="upload_fsqc - upload visualQC Freesurfer results"
 
#local variables
INPUT_DIR=""
 
#global variables
[ -s "$XNATAPIC_APPS/xnat.conf" ] && . "$XNATAPIC_APPS/xnat.conf"
[ -s "$XNATAPIC_HOME_APPS/xnat.conf" ] && . "$XNATAPIC_HOME_APPS/xnat.conf"
 
#parse arguments
for ((n=0; n<${#ARGS[@]}; n++)) ; do
	case "${ARGS[$n]}" in
		--help-short)
			echo "$HELP"
			exit 0
			;;
		--help)
			echo "$HELP"
			cat <<.EOF
 --help: show this help
 --qcdir <directory with visualQC results> [mandatory]
.EOF
			exit 0
			;;
		--qcdir)
			let n=n+1
			INPUT_DIR="${ARGS[$n]}"
			;;
		-*)
			echo "Warning: ignoring option or command ${ARGS[$n]}" >&2
			;;
		*)
			echo "Warning: ignoring option or command ${ARGS[$n]}" >&2
			;;
	esac
done
#checks
if [ -z "$INPUT_DIR" ]; then
	echo "Error: input directory is required" >&2
	exit 1
fi
#input files and directories
IMG_DIR="$INPUT_DIR/annot_visualizations"
RATINGS0="$INPUT_DIR/ratings/cortical_contour_rate_freesurfer_orig.mgz_ratings.all.csv"
END=$(tail -c 1 $RATINGS0)
RATINGS=$(mktemp -t fsqc_ratings.XXXXXXXX)
cp $RATINGS0 $RATINGS
if [ "$END" != "" ]; then echo "" >> $RATINGS; fi
#run
while read LINE; do
	XEXP=$(echo $LINE | awk -F"," '{print $1}')
	QCR=$(echo $LINE | awk -F"," '{print $2}')
	NOTE=$(echo $LINE | awk -F"," '{print $3}' | sed 's/Notes://')
	RESULT="{\"ResultSet\":{\"Result\":[{\"rating\":\"$QCR\",\"notes\":\"$NOTE\"}]}}"
	TEMP_RESULT_FILE=$(mktemp -t fsqc_results.XXXXXXXX)
	echo $RESULT > $TEMP_RESULT_FILE
	curl -f -X PUT -u "$USER:$PASSWORD" "$HOST/data/experiments/$XEXP/resources/fsqc"
	curl -f -X PUT -u "$USER:$PASSWORD" "$HOST/data/experiments/$XEXP/resources/fsqc/files/rating.json?overwrite=true" -F file="@$TEMP_RESULT_FILE"
	for IMG in $IMG_DIR/$XEXP*.tif; do
		NAME=$(basename $IMG)
		curl -f -X PUT -u "$USER:$PASSWORD" "$HOST/data/experiments/$XEXP/resources/fsqc/files/$NAME?overwrite=true" -F file="@$IMG"
	done
	rm $TEMP_RESULT_FILE
done < $RATINGS
#echo "So long, and thanks for all the fish!"

Consultar datos de QC

get_fsqc

get_fsqc.sh

#!/bin/bash
 
ARGS=( "$@" )
HELP="get_fsqc - get the results of Fresurfer QC"
 
#local variables
PROJ_ID=""
OUTPUT=""
 
#global variables
[ -s "$XNATAPIC_APPS/xnat.conf" ] && . "$XNATAPIC_APPS/xnat.conf"
[ -s "$XNATAPIC_HOME_APPS/xnat.conf" ] && . "$XNATAPIC_HOME_APPS/xnat.conf"
 
#parse arguments
for ((n=0; n<${#ARGS[@]}; n++)) ; do
	case "${ARGS[$n]}" in
		--help-short)
			echo "$HELP"
			exit 0
			;;
		--help)
			echo "$HELP"
			cat <<.EOF
 --help: show this help
 --project_id <project id> [mandatory]
 --output <output directory> [defaults to <project id>_fsqc.csv]
.EOF
			exit 0
			;;
		--project_id)
			let n=n+1
			PROJ_ID="${ARGS[$n]}"
			;;
		--output)
			let n=n+1
			OUTPUT="$(echo "${ARGS[$n]}" | sed 's/[ \n\r\t]\+/+/g')"
			;;
		-*)
			echo "Warning: ignoring option or command ${ARGS[$n]}" >&2
			;;
		*)
			echo "Warning: ignoring option or command ${ARGS[$n]}" >&2
			;;
	esac
done
 
#checks
if [ -z "$PROJ_ID" ]; then
	echo "Error: a project ID is required" >&2
	exit 1
fi
#defaults
[ -z "$OUTPUT" ] && OUTPUT="${PROJ_ID}_fsqc.csv"
#prepare
if [ -f $OUTPUT ]; then rm -rf $OUTPUT; fi
TEMP_SLIST=$(mktemp -t xsbjs.XXXXXXXX)
#run
if ! curl -f -X GET -u "$USER:$PASSWORD" "$HOST/data/projects/$PROJ_ID/subjects" 2>/dev/null | jq '.' > $TEMP_SLIST ; then
	echo "Error: server reported an error" >&2
	exit 1;
else
	TOTAL=$(cat $TEMP_SLIST | jq '.ResultSet.totalRecords' | sed 's/"//g')
	let TOTAL=TOTAL-1
	for SBJ in $(seq 0 $TOTAL); do 
		XSBJ=$(cat $TEMP_SLIST | jq ".ResultSet.Result[$SBJ].ID" | sed 's/"//g')
		XSBJ_LABEL=$(cat $TEMP_SLIST | jq ".ResultSet.Result[$SBJ].label" | sed 's/"//g')
		echo "Processing $XSBJ ... ($(($SBJ+1))/$(($TOTAL+1)))" 
		MRI=`curl -f -X GET -u "$USER:$PASSWORD" "$HOST/data/projects/$PROJ_ID/subjects/$XSBJ/experiments?xsiType=xnat:mrSessionData" 2>/dev/null | jq '.ResultSet.Result[].ID' | sed 's/"//g'`
		if [ $MRI ]; then
			TEMP_FSQC=$(mktemp -t xfsqc.XXXXXXXX)
			if curl -f -X GET -u "$USER:$PASSWORD" "$HOST/data/experiments/$MRI/resources/fsqc/files/rating.json" 2>/dev/null | jq '.' > $TEMP_FSQC ; then
				XRAT=$(cat $TEMP_FSQC | jq '.ResultSet.Result[].rating')
				XNOTES=$(cat $TEMP_FSQC | jq '.ResultSet.Result[].notes')
				if [ ! -z "$XRAT" ]; then echo "$XSBJ_LABEL, $XRAT, $XNOTES" >> $OUTPUT; fi
			fi
			rm $TEMP_FSQC
		fi
	done
fi
rm $TEMP_SLIST
echo "Bye, check results at $OUTPUT"

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Table of Contents

Opciones de XNAT CLI para el QC de Freesurfer

Bajar directorios de FS

Subir QC de FS

Consultar datos de QC

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Table of Contents

Opciones de XNAT CLI para el QC de Freesurfer

Bajar directorios de FS

Subir QC de FS

Consultar datos de QC

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