Making Brain Template Priors

Now that you have a template you need priors so that you can register the rest of the population to it. What follows is a script that I adapted from Nick Tustison’s antsCookTemplatePriorsExample. The OLDTEMP=${HOME}compute/templates/MICCAI2012-Multi-Atlas-Challenge-Data/ contains the images from here.
#!/bin/bash

#SBATCH --time=75:00:00
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --mem-per-cpu=32768M
#SBATCH -o /fslhome/username/logfiles/sobik/error_priors.txt
#SBATCH -e /fslhome/username/logfiles/sobik/output_priors.txt
#SBATCH -J "sobikpriors"
#SBATCH --mail-user=LavenderGooms@gmail.com
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL

export PBS_NODEFILE=`/fslapps/fslutils/generate_pbs_nodefile`
export PBS_JOBID=$SLURM_JOB_ID
export PBS_O_WORKDIR="$SLURM_SUBMIT_DIR"
export PBS_QUEUE=batch
export OMP_NUM_THREADS=$SLURM_CPUS_ON_NODE

export ANTSPATH=/fslhome/username/bin/antsbin/bin/
PATH=${ANTSPATH}:${PATH}

# user to change
HOME=/fslhome/username/

NEWTEMPHOME=${HOME}compute/dataset/template/
NEWTEMP=${NEWTEMPHOME}/T_template0.nii.gz
cd ${NEWTEMP}
DATA_DIR=${PWD}

OLDTEMP=${HOME}compute/templates/MICCAI2012-Multi-Atlas-Challenge-Data/
IMG=${OLDTEMP}/training-images/
IMGLABELS=${OLDTEMP}/training-labels/
mkdir ${NEWTEMPHOME}Output
OUT_DIR=${NEWTEMPHOME}/Output/

# Do antsCorticalThickness on template.  This is used to get the csf prior.
${ANTSPATH}antsCorticalThickness.sh -d 3 \
  -a ${NEWTEMP} \
  -e ${OLDTEMP}T_template0.nii.gz \
  -t ${OLDTEMP}T_template0_BrainCerebellum.nii.gz \
  -m ${OLDTEMP}T_template0_BrainCerebellumProbabilityMask.nii.gz \
  -f ${OLDTEMP}T_template0_BrainCerebellumExtractionMask.nii.gz \
  -p ${OLDTEMP}Priors2/priors%d.nii.gz \
  -o ${OUT_DIR}antsCT \
  -u 1

templateBrainMask=${OUT_DIR}antsCTBrainExtractionMask.nii.gz
templateBrain=${OUT_DIR}antsCTBrainExtractionBrain.nii.gz

${ANTSPATH}/ImageMath 3 $templateBrain m $templateBrainMask $NEWTEMP

# Do jlf labeling on extracted template brain.  This is used to get the rest of the priors
# including part of the csf prior.

${ANTSPATH}antsJointLabelFusion.sh -d 3  -c 5 -u 40:00:00 -v 16gb -w 40:00:00 -z 32gb \
-o ${OUT_DIR}/ants \
-t $templateBrain \
-g ${IMG}1000_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1000_3_glm.nii.gz \
-g ${IMG}1001_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1001_3_glm.nii.gz \
-g ${IMG}1002_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1002_3_glm.nii.gz \
-g ${IMG}1006_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1006_3_glm.nii.gz \
-g ${IMG}1007_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1007_3_glm.nii.gz \
-g ${IMG}1008_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1008_3_glm.nii.gz \
-g ${IMG}1009_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1009_3_glm.nii.gz \
-g ${IMG}1010_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1010_3_glm.nii.gz \
-g ${IMG}1011_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1011_3_glm.nii.gz \
-g ${IMG}1012_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1012_3_glm.nii.gz \
-g ${IMG}1013_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1013_3_glm.nii.gz \
-g ${IMG}1014_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1014_3_glm.nii.gz \
-g ${IMG}1015_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1015_3_glm.nii.gz \
-g ${IMG}1017_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1017_3_glm.nii.gz \
-g ${IMG}1036_3_BrainCerebellum.nii.gz -l ${IMGLABELS}1036_3_glm.nii.gz 

# convert labels to 6 tissue (4 in 2-D)
#  1. csf
#  2. gm
#  3. wm
#  4. subcortical gm
#  5. brain stem
#  6. cerebellum

csfLabels=( 4 46 49 50 51 52 )
wmLabels=( 44 45 )
corticalLabels=( 31 32 42 43 47 48 )  # also anything >= 100
subcorticalLabels=( 23 30 36 37 55 56 57 58 59 60 61 62 63 64 75 76 )
brainstemLabels=( 35 )
cerebellumLabels=( 11 38 39 40 41 71 72 73 )
 
tmp=${OUT_DIR}/tmpForRelabeling.nii.gz
jlf=${OUT_DIR}/antsLabels.nii.gz
jlf6=${OUT_DIR}/antsjlf_6Labels.nii.gz

ThresholdImage 3 $jlf $jlf6 100 207 2 0

echo "csf: "
for(( j=0; j<${#csfLabels[@]}; j++ ));
  do
    echo ${csfLabels[$j]}
    ${ANTSPATH}/ThresholdImage 3 $jlf $tmp ${csfLabels[$j]} ${csfLabels[$j]} 1 0
    ${ANTSPATH}/ImageMath 3 $jlf6 + $tmp $jlf6
  done

echo "cortex: "
for(( j=0; j<${#corticalLabels[@]}; j++ ));
  do
    echo ${corticalLabels[$j]}
    ${ANTSPATH}/ThresholdImage 3 $jlf $tmp ${corticalLabels[$j]} ${corticalLabels[$j]} 2 0
    ${ANTSPATH}/ImageMath 3 $jlf6 + $tmp $jlf6
  done

echo "white matter: "
for(( j=0; j<${#wmLabels[@]}; j++ ));
  do
    echo ${wmLabels[$j]}
    ${ANTSPATH}/ThresholdImage 3 $jlf $tmp ${wmLabels[$j]} ${wmLabels[$j]} 3 0
    ${ANTSPATH}/ImageMath 3 $jlf6 + $tmp $jlf6
  done

echo "sub-cortex: "
for(( j=0; j<${#subcorticalLabels[@]}; j++ ));
  do
    echo ${subcorticalLabels[$j]}
    ${ANTSPATH}/ThresholdImage 3 $jlf $tmp ${subcorticalLabels[$j]} ${subcorticalLabels[$j]} 4 0
    ${ANTSPATH}/ImageMath 3 $jlf6 + $tmp $jlf6
  done

echo "brain stem: "
for(( j=0; j<${#brainstemLabels[@]}; j++ ));
  do
    echo ${brainstemLabels[$j]}
    ${ANTSPATH}/ThresholdImage 3 $jlf $tmp ${brainstemLabels[$j]} ${brainstemLabels[$j]} 5 0
    ${ANTSPATH}/ImageMath 3 $jlf6 + $tmp $jlf6
  done

echo "cerebellum: "
for(( j=0; j<${#cerebellumLabels[@]}; j++ ));
  do
    echo ${cerebellumLabels[$j]}
    ${ANTSPATH}/ThresholdImage 3 $jlf $tmp ${cerebellumLabels[$j]} ${cerebellumLabels[$j]} 6 0
    ${ANTSPATH}/ImageMath 3 $jlf6 + $tmp $jlf6
  done

# now convert each to a probability map

antsCtCsfPrior=${OUT_DIR}/antsCTPrior1.nii.gz
${ANTSPATH}/SmoothImage 3 ${OUT_DIR}/antsCTBrainSegmentationPosteriors1.nii.gz 1 $antsCtCsfPrior

for(( j=1; j<=6; j++ ));
  do
    prior=${OUT_DIR}/prior${j}.nii.gz
    ${ANTSPATH}/ThresholdImage 3 $jlf6 $prior $j $j 1 0
    ${ANTSPATH}/SmoothImage 3 $prior 1 $prior
  done

${ANTSPATH}/ImageMath 3 ${OUT_DIR}/prior1.nii.gz max ${OUT_DIR}/prior1.nii.gz $antsCtCsfPrior

# subtract out csf prior from all other priors

prior1=${OUT_DIR}/prior1.nii.gz
for(( j=2; j<=6; j++ ));
  do
    prior=${OUT_DIR}/prior${j}.nii.gz
    ${ANTSPATH}/ImageMath 3 $prior - $prior $prior1
    ${ANTSPATH}/ThresholdImage 3 $prior $tmp 0 1 1 0
    ${ANTSPATH}/ImageMath 3 $prior m $prior $tmp
  done

cp $templateBrainMask ${NEWTEMPHOME}T_template0_BrainCerebellumExtractionMask.nii.gz
cp $templateBrain ${NEWTEMPHOME}T_template0_BrainCerebellum.nii.gz
${ANTSPATH}/SmoothImage 3 $templateBrainMask 1 ${NEWTEMPHOME}T_template0_BrainCerebellumProbabilityMask.nii.gz
mkdir ${NEWTEMPHOME}Priors
cp ${OUTD_DIR}prior*.nii.gz ${NEWTEMPHOME}/Priors/
rm $tmp

echo "Priors are cooked.  They can be found in ${OUT_DIR}"
This script basically calls antsCorticalThickness.sh to get a csf prior and then uses antsJointLabelFusion.sh to create an atlas of the template brain. ThresholdImage and ImageMath are used to add labels that correlate to a given prior into one label. SmoothImage is then used to change the label from a simple binary mask to a prior. Feel free to look at the script in more detail, but thats the basic gist of the entire thing.
Once you’ve generated your priors you may want to clean things up a bit. The important thing is that you end up with the following files.
template_folder
|--Labels
|  |--antsjlf_6Labels.nii.gz
|  |--antsLabels.nii.gz
|
|--Priors
|  |--priors1.nii.gz
|  |--priors2.nii.gz
|  |--priors3.nii.gz
|  |--priors4.nii.gz
|  |--priors5.nii.gz
|  |--priors6.nii.gz
|
|--T_template0_BrainCerebellum.nii.gz
|--T_template0_BrainCerebellumExtractionMask.nii.gz
|--T_template0_BrainCerebellumProbabilityMask.nii.gz
|--T_template0.nii.gz

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