16 lines
319 B
Text
16 lines
319 B
Text
$ cat << EOT > code/brain_extraction.sh
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# enable FSL
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. /etc/fsl/5.0/fsl.sh
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# obtain all inputs
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datalad get \$@
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# perform brain extraction
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count=1
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for nifti in \$@; do
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subdir="sub-\$(printf %03d \$count)"
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mkdir -p \$subdir
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echo "Processing \$nifti"
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bet \$nifti \$subdir/anat -m
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count=\$((count + 1))
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done
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EOT
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