Align and Bias Correct Your Brain!

Once you’re files are ready to by preprocessed (Yes, there’s a word for the processing that takes place before the processing). They need to be aligned to a common image space.
Here’s my handy script:
#!/bin/bash

#SBATCH --time=30:00
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --mem-per-cpu=8192M
#SBATCH -o /fslhome/zach8769/logfiles/oasis_longitudinal/output_prepT1_0.txt
#SBATCH -e /fslhome/zach8769/logfiles/oasis_longitudinal/error_prepT1_0.txt
#SBATCH -J "prepT1_0"
#SBATCH --mail-user=GalileoHumpkins@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

ROOT=/fslhome/GalileoHumpkins/
DATASET=${ROOT}compute/oasis_longitudinal/
TEMPLATE=${ROOT}compute/templates/MICCAI2012-Multi-Atlas-Challenge-Data/
export ANTSPATH=/fslhome/zach8769/bin/antsbin/bin/
PATH=${ANTSPATH}:${PATH}

IFS=$'\n'
array=( $(find ${DATASET}/*/t1/*/ -type f -name t1.nii.gz) )
for i in 0;
  do
  SUB=$(dirname ${array[$i]})

  ${ANTSPATH}antsRegistrationSyNQuick.sh -d 3 \
    -f ${TEMPLATE}T_template0.nii.gz \
    -m ${SUB}/t1.nii.gz \
    -o ${SUB}/rigid_ \
    -t r

  N4BiasFieldCorrection -d 3 \
    -i ${SUB}/rigid_Warped.nii.gz \
    -o ${SUB}/n4.nii.gz \
    -s 8 -b [200] -c [50x50x50x50,0.000001]
    
  N4BiasFieldCorrection -d 3 \
    -i ${SUB}/n4.nii.gz \
    -o ${SUB}/n4.nii.gz \
    -s 4 -b [200] -c [50x50x50x50,0.000001]

  N4BiasFieldCorrection -d 3 \
    -i ${SUB}/n4.nii.gz \
    -o ${SUB}/n4.nii.gz \
    -s 2 -b [200] -c [50x50x50x50,0.000001]

  ResampleImage 3 \
    ${SUB}/n4.nii.gz \
    ${SUB}/n4_resliced.nii.gz 1x1x1

  rm ${SUB}/rigid_0GenericAffine.mat
  rm ${SUB}/rigid_InverseWarped.nii.gz
done
Th N4BiasFieldCorrection command accounts for different intensities in the scan that result from bias in the signal as a result of their location in 3 dimensions (there are a lot more details but they’re beyond the scope of this post). The ResampleImage command ensures that all images have the same voxel spacing. As a whole, this script ensures that image spacing and intensity is as comparable as possible before any further processes that compare anatomical differences are used.

After
Before

Comments

Post a Comment

Popular posts from this blog

Medical School: Week 1

Image
Monday : We had a problem based learning (PBL) case that was meant to exercise our public health and disease prevention knowledge. Besides that most of classes were just introduction to various topics and what's expected of us. After all of our classes were over we had the opportunity to sign up for special interest groups that occasionally meet and teach about various specialties and service opportunities during lunch. I signed up for several and got to do an ultrasound on some guys arm. He showed me what his artery looked like on the machine. I thoght it was pretty darn cool. Tuesday : Classes technically ended at 12:00, although I didn't get home until about 4:00.  We learned a little bit about statistics used for screening for diseases in our first lecture. In our second lecture a fourth year medical student taught us about societal determinants of health. As one student put it, "He talked so fast he sounded like Eminem." We then spent the remaining time in sm...
Read more

Getting Started in Rochester

Image
Recently we moved to Rochester New York and brought an entire tribe with us to help us move in (AKA my family and Lexi's family). We went to Niagara falls where Addie was scared of the water and Zoey tried to lick the water. We went to the beach where I fell asleep in the sand and my mom got algae stuck in her swimsuit. We picked fresh berries at a local farm where my brother in law Aaron and I ate a month's worth of blueberries. We went to the Sacred Grove and gave the where my dad and I suggested to the sister missionaries some improved names for their stories ("The Subterfuge"). We visited the Erie Canal where my mother in law serenaded us with her beautiful old-timey song. It was a truly magical time filled with visits to Boston Market and Dunkin' Donuts (did you know America runs on Dunkin'?!). But now we're back to reality and trying to get use to our new life here. Here are some things since that have happened since the tribe left: I laughed ...
Read more