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