Delete WMH_perivent_deep_classification.sh to be replaced with new version

WMH_perivent_deep_classification.sh

-#!/bin/bash
-#
-# Script name: WMH_perivent_deep_classification
-#
-# Description: Script to calculate volume of total, periventricular and deep white matter hyperintensities
-#
-# Authors: Ludovica Griffanti, Mark Jenkinson
-#
-# Copyright 2021 University of Oxford
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-set -e
-# set -x
-
-if [ $# -lt 5 ] ; then
-  echo "Usage:  `basename $0` <thresholded_binarised_WMH_map> <ventricles_mask> <minclustersize> <do_stats 0 1 2> <outputdir>"
-  echo " This script separates WMH into periventricular and deep WMH, saves two separate binary images (perivent_map and deepwm_map) and calculates volume of total and separate WMHs"
-  echo "      INPUT 1: <thresholded_binarised_WMH_map>"
-  echo " This script was created as postprocessing after WMH segmentation with BIANCA. The input file requested is BIANCA output thresholded at the desired threshold and binarised,  e.g. running:"
-  echo "fslmaths BIANCA_output -thr 0.9 -bin BIANCA_out_thr09_bin"
-  echo "and using BIANCA_out_thr09_bin as input for this script"
-  echo "      INPUT 2: <ventricles_mask>"
-  echo " If make_bianca_mask.sh was used to create an exlusion mask for BIANCA output, the ventricle mask to use is the file ventmask.nii.gz"
-  echo " If T1 and FLAIR were not in the same space, ventricle mask needs to be registered to FLAIR (and binarised)"
-  echo "      INPUT 3: minimum cluster (volume) size (in voxels) to consider"
-  echo " Use 0 for no cluster thresholding"
-  echo "      INPUT 4: <do_stats 0 1 2>"
-  echo "if 0 it will only produce the images and not calculate volumes"
-  echo "if 1 it will calculate volumes for total, periventricular and deep WMH and display on the screen"
-  echo "if 2 it will calculate volumes and save them in the file WMH_tot_pvent_deep_10mm.txt"
-  exit 0
-fi
-
-bianca_out_bin=$1
-ventricle_mask=$2
-minclustersize=$3
-do_stats=$4
-outdir=$5
-
-outputdir=${outdir}/pwmh_dwmh_output
-if [ ! -d $outputdir ]; then
-    mkdir $outputdir
-fi
-
-# Cluster thresholding if needed
-if [ ${minclustersize} -gt 0 ]; then
-# create indexed version of all the lesions in the mask (above minclustersize)
-cluster --in=$bianca_out_bin --thresh=0.05 --oindex=$outputdir/bianca_out_mincluster${minclustersize} --connectivity=6 --no_table --minextent=${minclustersize}
-fslmaths $outputdir/bianca_out_mincluster${minclustersize} -bin $outputdir/bianca_out_mincluster${minclustersize}
-bianca_out_bin=$outputdir/bianca_out_mincluster${minclustersize}
-fi
-
-# CRITERION: Distance from ventricles (10 mm)
-distancemap -i $ventricle_mask -m $bianca_out_bin -o $outputdir/bianca_out_bin_distvent
-# If a lesion is within 10 mm from the ventricles is periventricular, if not, it is deep.
-# generating deep mask first because in case of overlap between registered ventmask and WMH, that voxel will be 0,
-# not ending up in bianca_out_bin_distvent and being misclassified as deep in the subtraction.
-# Here I take everything above 9.99 as deep and generate pvent by subtraction from the original WMH, not the _distvent one.
-
-fslmaths ${outputdir}/bianca_out_bin_distvent -thr 9.99 -bin ${outputdir}/deepwm_map_10mm
-fslmaths $bianca_out_bin -sub ${outputdir}/deepwm_map_10mm $outputdir/perivent_map_10mm
-
-# volumes extraction
-if [ $do_stats=1 ] | [ $do_stats=2 ] ; then
-    tot_vol=`fslstats $bianca_out_bin -V | awk '{print $2}'`
-    pvent_vol_10mm=`fslstats $outputdir/perivent_map_10mm -V | awk '{print $2}'`
-    deep_vol_10mm=`fslstats $outputdir/deepwm_map_10mm -V | awk '{print $2}'`
-
-    if [ $do_stats=2 ] ; then
-	echo $tot_vol $pvent_vol_10mm $deep_vol_10mm >>  $outputdir/WMH_tot_pvent_deep_10mm.txt
-    elif [ $do_stats=1 ] ; then
-	echo "tot_volume= $tot_vol DISTANCE10mm:pvent_vol_10mm= $pvent_vol_10mm deep_vol_10mm= $deep_vol_10mm "
-    fi 
-fi
-