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