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- #!/bin/bash
- set -e
- set -u
- subj=$1
- t1dir="${subj}/t1w"
- bolddir="${subj}/bold3Tp2"
- mkdir -p "${bolddir}/in_t1w"
- mkdir -p "${t1dir}/in_bold3Tp2"
- #$FSLDIR/bin/flirt -dof 6 \
- # -in ${bolddir}/brain \
- # -ref ${t1dir}/brain_nobias \
- # -omat "${bolddir}/in_t1w/xfm_6dof.mat" \
- # -out "${bolddir}/in_t1w/brain"
- #
- #$FSLDIR/bin/convert_xfm \
- # -omat "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
- # -inverse "${bolddir}/in_t1w/xfm_6dof.mat"
- #
- #$FSLDIR/bin/flirt \
- # -in "${t1dir}/brain_nobias" \
- # -ref "${bolddir}/brain" \
- # -applyxfm \
- # -init "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
- # -out "${t1dir}/in_bold3Tp2/brain"
- #
- # occiptal focus
- #
- $FSLDIR/bin/fslmaths \
- /usr/share/data/mni-structural-atlas/MNI/MNI-maxprob-thr0-2mm.nii.gz \
- -thr 5 -uthr 5 -bin -dilF -dilF \
- ${t1dir}/in_mni152/dil_occ_mask.nii.gz
- $FSLDIR/bin/flirt \
- -in ${t1dir}/in_mni152/dil_occ_mask.nii.gz \
- -ref "${t1dir}/brain" \
- -applyxfm \
- -init "${t1dir}/in_mni152/tmpl2subj.mat" \
- -out "${t1dir}/dil_occ_mask"
- $FSLDIR/bin/flirt \
- -in "${t1dir}/dil_occ_mask" \
- -ref "${bolddir}/brain" \
- -applyxfm \
- -init "${t1dir}/in_bold3Tp2/xfm_6dof.mat" \
- -out "${bolddir}/dil_occ_mask"
- $FSLDIR/bin/flirt -dof 6 \
- -in ${bolddir}/brain \
- -ref ${t1dir}/brain_nobias \
- -refweight ${t1dir}/dil_occ_mask \
- -inweight ${bolddir}/dil_occ_mask \
- -init "${bolddir}/in_t1w/xfm_6dof.mat" \
- -searchrx -20 20 \
- -searchry -20 20 \
- -searchrz -20 20 \
- -omat "${bolddir}/in_t1w/xfm_6dof_occ.mat" \
- -out "${bolddir}/in_t1w/brain_occ"
- $FSLDIR/bin/convert_xfm \
- -omat "${t1dir}/in_bold3Tp2/xfm_6dof_occ.mat" \
- -inverse "${bolddir}/in_t1w/xfm_6dof_occ.mat"
- $FSLDIR/bin/flirt \
- -in "${t1dir}/brain_nobias" \
- -ref "${bolddir}/brain" \
- -applyxfm \
- -init "${t1dir}/in_bold3Tp2/xfm_6dof_occ.mat" \
- -out "${t1dir}/in_bold3Tp2/brain_occ"
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