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@@ -0,0 +1,31 @@
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+#!/bin/bash
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+
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+set -e
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+set -u
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+
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+subj=$1
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+
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+b7dir="${subj}/bold7Tp1"
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+b3dir="${subj}/bold3Tp2"
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+
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+mkdir -p "${b3dir}/in_bold7Tp1"
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+mkdir -p "${b7dir}/in_bold3Tp2"
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+
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+
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+$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 "${b7dir}/in_bold3Tp2/brain"
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+
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+$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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+
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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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