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@@ -11,66 +11,88 @@ bolddir="${subj}/bold3Tp2"
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mkdir -p "${bolddir}/in_t1w"
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mkdir -p "${t1dir}/in_bold3Tp2"
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-
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+## old coreg
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#$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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-#
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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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+ #-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 "${t1dir}/in_bold3Tp2/brain"
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+ #-in "${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 "${t1dir}/in_bold3Tp2/brain"
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-#
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-# occiptal focus
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-#
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+# coregister t1w to bold ..
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+$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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-$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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- ${t1dir}/in_mni152/dil_occ_mask.nii.gz
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+# .. and inverse transformation matrix ..
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+$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 ${t1dir}/in_mni152/dil_occ_mask.nii.gz \
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- -ref "${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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+ -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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-$FSLDIR/bin/flirt \
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- -in "${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 "${bolddir}/in_t1w/xfm_6dof_occ.mat"
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+##
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+## occiptal focus
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+##
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-$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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+#$FSLDIR/bin/fslmaths \
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+ #/usr/share/data/mni-structural-atlas/MNI/MNI-maxprob-thr0-2mm.nii.gz \
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+ #-thr 5 -uthr 5 -bin -dilF -dilF \
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+ #${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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