41 lines
1.1 KiB
Bash
Executable file
41 lines
1.1 KiB
Bash
Executable file
#!/bin/bash
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# Author: Michael Hanke <michael.hanke@gmail.com>
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# License: MIT
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set -e
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set -u
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# fake test for FSL
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ignore=$FSLDIR
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inbold=$(readlink -f $1) || true
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initref=$(readlink -f $2) || true
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finalref=$(readlink -f $3) || true
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finalxfm=$(readlink -f $4) || true
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outbold=$(readlink -m $5)
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initflirtopts=${6:--dof 6}
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for f in "$inbold" "$initref" "$finalref" "$finalxfm"; do
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if [ -z "$f" ]; then
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echo "File not found '$1'"
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exit 1
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fi
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done
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outbolddir=$(dirname "${outbold}")
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mkdir -p "$outbolddir"
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wdir=$(mktemp -d --suffix=7to3reslice)
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echo $wdir
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trap "rm -rf $wdir" SIGINT SIGTERM
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cd "$wdir"
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$FSLDIR/bin/fslroi "$inbold" bold 0 1
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$FSLDIR/bin/bet bold bold_brain -Z -f 0.1
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$FSLDIR/bin/flirt ${initflirtopts} -in bold_brain -ref $initref -omat bold2brain.mat
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$FSLDIR/bin/convert_xfm -omat bold2final.mat -concat "$finalxfm" bold2brain.mat
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#$FSLDIR/bin/flirt -in bold_brain -ref "$finalref" -applyxfm -init bold2final.mat -out "$outbold" -interp sinc
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$FSLDIR/bin/flirt -in "$inbold" -ref "$finalref" -applyxfm -init bold2final.mat -out "$outbold" -interp sinc
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cd -
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rm -rf "$wdir"
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