12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091 #!/bin/sh # # # This file is part of MIA - a toolbox for medical image analysis # Copyright (c) Leipzig, Madrid 1999-2013 Gert Wollny # # MIA is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, see . # # # call this program like: # # brainmash.sh # #supported file formats (all only gray scale) # Analyze # inria # vff # vista # vtk print_usage() { echo Usage: echo " brainmash.sh " echo exit 1 } if [ "x$1" = "x" ]; then echo Error: input file missing print_usage fi if [ "x$2" = "x" ]; then echo Error: output file missing print_usage fi infile=$1 outfile=$2 #white matter probability \in [0,1] wmprob=0.7 #erode shape for initial wm mask, # possible values: 6n 18n 26n, [sphere:r=N] (N > 0) erode_shape=6n #growmask shape, possible values see erode_shape shape=18n #intensity threshhold for mask growing thresh=30 #final closing shape, possible values see erode_shape close_shape=[sphere:r=3] #final opening shape, possible values see erode_shape open_shape=[sphere:r=3] # segment the input image into 3 classes mia-fuzzysegment3d -i $infile -o b0.v -c cls.v -n 3 -V message && \ mia-3dimageselect -i cls.v -o wmprob.v -n 2 && \ mia-3dimagefilter -i wmprob.v -o$outfile \ -V message \ binarize:min=$wmprob \ erode:shape=${erode_shape} \ label \ selectbig \ growmask:ref=b0.v,min=${thresh},shape=${shape} \ close:shape=${close_shape}\ open:shape=${open_shape}\ mask:input=b0.v || \ echo "Error processing '\$infile'" #rm -f b0.v cls.v wmprob.v