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create_MM_labelmaps.sh
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create_MM_labelmaps.sh
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#!/usr/bin/env bash
#
# MM reorg of hippocampus regions
#
# We have to get these from the hires resampled images:
# lh.hippoAmygLabels-T1.v22.mgz
# rh.hippoAmygLabels-T1.v22.mgz
# Both hemispheres are labeled with the same codes.
#
# Label info is in $FREESURFER_HOME/FreeSurferColorLUT.txt
#
# Resample with mri_vol2vol
##############################################################################
# MMAP anterior/posterior
#
# Anterior (1)
# 233 presubiculum-head
# 235 subiculum-head
# 237 CA1-head
# 239 CA3-head
# 241 CA4-head
# 243 GC-ML-DG-head
# 245 molecular_layer_HP-head
#
# Posterior (2)
# 226 Hippocampal_tail
# 234 presubiculum-body
# 236 subiculum-body
# 238 CA1-body
# 240 CA3-body
# 242 CA4-body
# 244 GC-ML-DG-body
# 246 molecular_layer_HP-body
#
# Discard (0)
# 203 parasubiculum
# 211 HATA
# 212 fimbria
# 215 hippocampal-fissure
# 7... amygdala
for hemi in lh rh ; do
mri_binarize \
--i "${mri_dir}/${hemi}.hippoAmygLabels-T1.v22.mgz" \
\
--replace 233 1 \
--replace 235 1 \
--replace 237 1 \
--replace 239 1 \
--replace 241 1 \
--replace 243 1 \
--replace 245 1 \
\
--replace 226 2 \
--replace 234 2 \
--replace 236 2 \
--replace 238 2 \
--replace 240 2 \
--replace 242 2 \
--replace 244 2 \
--replace 246 2 \
\
--replace 203 0 \
--replace 211 0 \
--replace 212 0 \
--replace 215 0 \
\
--replace 7001 0 \
--replace 7003 0 \
--replace 7005 0 \
--replace 7006 0 \
--replace 7007 0 \
--replace 7008 0 \
--replace 7009 0 \
--replace 7010 0 \
--replace 7015 0 \
\
--o "${tmp_dir}"/${hemi}.hippoLabels-T1.v22.MMAP.mgz
mri_vol2vol --nearest --regheader \
--mov "${tmp_dir}"/${hemi}.hippoLabels-T1.v22.MMAP.mgz \
--targ "${mri_dir}"/${hemi}.hippoAmygLabels-T1.v22.FSvoxelSpace.mgz \
--o "${tmp_dir}"/${hemi}.hippoLabels-T1.v22.MMAP.FSVoxelSpace.mgz
done
# Make corresponding label file
cat <<EOF > "${tmp_dir}/hippoLabels-T1.v22.MMAP.csv"
Label,Region
1,Anterior-Hippocampus
2,Posterior-Hippocampus
EOF
##############################################################################
# MMHBT head/body/tail
#
# Head-CA (1)
# 235 subiculum-head
# 237 CA1-head
# 239 CA3-head
# 245 molecular_layer_HP-head
#
# Head-DG (2)
# 241 CA4-head
# 243 GC-ML-DG-head
#
# Head-subiculum (3)
# 233 presubiculum-head
#
# Body-CA (4)
# 236 subiculum-body
# 238 CA1-body
# 240 CA3-body
# 246 molecular_layer_HP-body
#
# Body-DG (5)
# 242 CA4-body
# 244 GC-ML-DG-body
#
# Body-subiculum (6)
# 234 presubiculum-body
#
# Tail (7)
# 226 Hippocampal_tail
#
# Discard (0)
# 203 parasubiculum
# 211 HATA
# 212 fimbria
# 215 hippocampal-fissure
# 7... amygdala
for hemi in lh rh ; do
mri_binarize \
--i "${mri_dir}/${hemi}.hippoAmygLabels-T1.v22.mgz" \
\
--replace 235 1 \
--replace 237 1 \
--replace 239 1 \
--replace 245 1 \
\
--replace 241 2 \
--replace 243 2 \
\
--replace 233 3 \
\
--replace 236 4 \
--replace 238 4 \
--replace 240 4 \
--replace 246 4 \
\
--replace 242 5 \
--replace 244 5 \
\
--replace 234 6 \
\
--replace 226 7 \
\
--replace 203 0 \
--replace 211 0 \
--replace 212 0 \
--replace 215 0 \
\
--replace 7001 0 \
--replace 7003 0 \
--replace 7005 0 \
--replace 7006 0 \
--replace 7007 0 \
--replace 7008 0 \
--replace 7009 0 \
--replace 7010 0 \
--replace 7015 0 \
\
--o "${tmp_dir}"/${hemi}.hippoLabels-T1.v22.MMHBT.mgz
mri_vol2vol --nearest --regheader \
--mov "${tmp_dir}"/${hemi}.hippoLabels-T1.v22.MMHBT.mgz \
--targ "${mri_dir}"/${hemi}.hippoAmygLabels-T1.v22.FSvoxelSpace.mgz \
--o "${tmp_dir}"/${hemi}.hippoLabels-T1.v22.MMHBT.FSVoxelSpace.mgz
done
# Make corresponding label file
cat <<EOF > "${tmp_dir}/hippoLabels-T1.v22.MMHBT.csv"
Label,Region
1,Head-CA
2,Head-DG
3,Head-subiculum
4,Body-CA
5,Body-DG
6,Body-subiculum
7,Tail
EOF