31 lines
645 B
Bash
Executable file
31 lines
645 B
Bash
Executable file
#!/bin/bash
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set -e
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set -u
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subj=$1
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b7dir="${subj}/bold7Tp1"
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b3dir="${subj}/bold3Tp2"
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mkdir -p "${b3dir}/in_bold7Tp1"
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mkdir -p "${b7dir}/in_bold3Tp2"
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$FSLDIR/bin/flirt -dof 6 \
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-forcescaling -paddingsize 10 -minsampling 1 -bins 256 \
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-in ${b7dir}/brain \
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-ref ${b3dir}/brain \
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-omat "${b7dir}/in_bold3Tp2/xfm_6dof.mat" \
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-out "${b7dir}/in_bold3Tp2/brain"
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$FSLDIR/bin/convert_xfm \
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-omat "${b3dir}/in_bold7Tp1/xfm_6dof.mat" \
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-inverse "${b7dir}/in_bold3Tp2/xfm_6dof.mat"
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$FSLDIR/bin/flirt \
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-in "${b3dir}/brain" \
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-ref "${b7dir}/brain" \
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-applyxfm \
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-init "${b3dir}/in_bold7Tp1/xfm_6dof.mat" \
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-out "${b3dir}/in_bold7Tp1/brain"
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