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@@ -0,0 +1,76 @@
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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=$1
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+
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+t1dir="${subj}/t1w"
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+bolddir="${subj}/bold3Tp2"
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+
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+mkdir -p "${bolddir}/in_t1w"
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+mkdir -p "${t1dir}/in_bold3Tp2"
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+
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+
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+#$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 "${bolddir}/in_t1w/brain"
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+#
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+#$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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+#
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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 "${t1dir}/in_bold3Tp2/brain"
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+
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+#
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+# occiptal focus
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+#
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+
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+$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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+ ${t1dir}/in_mni152/dil_occ_mask.nii.gz
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+
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+$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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+
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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 "${bolddir}/dil_occ_mask"
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+
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+$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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+
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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 "${bolddir}/in_t1w/xfm_6dof_occ.mat"
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+
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+$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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