Chapter 7 ANTS Cortical Thickness
Log onto the remote computer. Remember you will be using the preprocessed T1 image found under ‘/work/${username}/data/ACAP/prepAnat/’.
7.1 Download Template
On the remote computer, download the OASIS template.
mkdir ~/templates
cd ~/templates
wget https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/3133832/Oasis.zip
unzip Oasis.zip && rm -rf Oasis.zip
If the template directory isn’t labeled OASIS, rename the directory.
cd ~/templates
mv MICCAI2012-Multi-Atlas-Challenge-Data/ OASIS/
7.2 Job Script
Still on the remote computer, create job script. The output files will have to be placed under a mindboggle directory, ‘/work/ashley.ware/data/ACAP/mindboggle/ants_subjects/’.
vi ~/scripts/ACAP/antsCT-job.sh
Copy and paste.
#!/bin/bash
#SBATCH --time=15:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=16G # memory per CPU core
# LOAD ENVIRONMENTAL VARIABLES
username=`id -un`
export ANTSPATH=/home/${username}/apps/ants/bin/
PATH=${ANTSPATH}:${PATH}
# INSERT CODE, AND RUN YOUR PROGRAMS HERE
DATA=/work/${username}/data/ACAP/prepAnat/${1}
TPL=~/templates/OASIS
mkdir -p /work/${username}/data/ACAP/mindboggle/ants_subjects/${1}/
antsCorticalThickness.sh \
-d 3 \
-a ${DATA}/${1}_T1w.nii.gz \
-e ${TPL}/T_template0.nii.gz \
-t ${TPL}/T_template0_BrainCerebellum.nii.gz \
-m ${TPL}/T_template0_BrainCerebellumProbabilityMask.nii.gz \
-f ${TPL}/T_template0_BrainCerebellumExtractionMask.nii.gz \
-p ${TPL}/Priors2/priors%01d.nii.gz \
-q 1 \
-n 6 \
-x 6 \
-o /work/${username}/data/ACAP/mindboggle/ants_subjects/${1}/ants
7.3 Batch Script
First check that your subjid
are correct.
for i in $(find /work/ashley.ware/data/ACAP/prepAnat/ -name "*T1w.nii.gz"); do
subjid=`echo $i | cut -d "/" -f7`
echo $subjid
done
If everything is correct then you can create your batch file.
Create batch script.
vi ~/scripts/ACAP/antsCT-batch.sh
Copy and paste.
#!/bin/bash
curTime=`date +"%Y%m%d-%H%M%S"`
username=`id -un`
mkdir -p ~/logfiles/ACAP/${curTime}
for i in $(find /work/${username}/data/ACAP/prepAnat/ -name "*T1w.nii.gz"); do
subjid=`echo $i | cut -d "/" -f7`
sbatch \
-o ~/logfiles/ACAP/${curTime}/output_${subjid}.txt \
-e ~/logfiles/ACAP/${curTime}/error_${subjid}.txt \
~/scripts/ACAP/antsCT-job.sh \
${subjid}
sleep 1
done
7.4 Submit Jobs with Batch Script
Submit jobs.
sh ~/scripts/ACAP/antsCT-batch.sh
You can check the status of your jobs by checking if it is running or pending.
squeue
You can check the outputs.
tail -n 5 ~/logfiles/ACAP/<date>/output*
7.5 Directory Structure
The final data structure will look like this.
/work/ashley.ware/data/ACAP/mindboggle/
|–– ants_subjects/
|–– sub-ACAP1001_ses-BL/
|–– antsACTStage1Complete.txt
|–– antsACTStage2Complete.txt
|–– antsACTStage3Complete.txt
|–– antsACTStage4Complete.txt
|–– antsACTStage5Complete.txt
|–– antsACTStage6Complete.txt
|–– antsBrainExtractionMask.nii.gz
|–– antsBrainNormalizedToTemplate.nii.gz
|–– antsBrainSegmentation0N4.nii.gz
|–– antsBrainSegmentationConvergence.txt
|–– antsBrainSegmentation.nii.gz
|–– antsBrainSegmentationPosteriors1.nii.gz
|–– antsBrainSegmentationPosteriors2.nii.gz
|–– antsBrainSegmentationPosteriors3.nii.gz
|–– antsBrainSegmentationPosteriors4.nii.gz
|–– antsBrainSegmentationPosteriors5.nii.gz
|–– antsBrainSegmentationPosteriors6.nii.gz
|–– antsBrainSegmentationTiledMosaic.png
|–– antsbrainvols.csv
|–– antsCorticalThickness.nii.gz
|–– antsCorticalThicknessNormalizedToTemplate.nii.gz
|–– antsCorticalThicknessTiledMosaic.png
|–– antsExtractedBrain0N4.nii.gz
|–– antsRegistrationTemplateBrainMask.nii.gz
|–– antsSubjectToTemplate0GenericAffine.mat
|–– antsSubjectToTemplate1Warp.nii.gz
|–– antsSubjectToTemplateLogJacobian.nii.gz
|–– antsTemplateToSubject0Warp.nii.gz
|–– antsTemplateToSubject1GenericAffine.mat
7.6 Download Directory / Sync Directory with Arc
Back on your local computer make sure you have the directory already.
mkdir -p /Volumes/bobo/data/ACAP/mindboggle/ants_subjects
Then sync the data from the remote computer to your local computer.
rsync -rauv \
ashley.ware@arc.ucalgary.ca:/work/ashley.ware/data/ACAP/mindboggle/ants_subjects/ \
/Volumes/bobo/data/ACAP/mindboggle/ants_subjects/