Research


T1 Processing:
These posts describe some of the most important steps in preprocessing T1 weighted MRI scans for statistical analysis. The focus is on the use of advanced normalization tools (ANTs) normalize and register images in order to produce images that can later be statistically analyzed. Automated production of diffeomorphic, cortical thickness, and automated tracing of regions of interest (ROIs) are produced through these processes.


Statistics:
These posts demonstrate how to perform basic statistics with an emphasis on the application of statistics to neuroimaging. Much of this is still under development.



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Align and Bias Correct Your Brain!

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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-Mu...
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Making a Brain Template

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My last post was on how to obtain a representative sample to create a brain template. This post shows how to create the actual template. This step is fairly straightforward because most of the heavy lifting is already performed by antsMultivariateTemplateContstruction.sh . Here’s the entirety of the script so that you have an idea of how it all looks together. #!/bin/bash #SBATCH --time=75:00:00 #SBATCH --ntasks=1 #SBATCH --nodes=1 #SBATCH --mem-per-cpu=32768M #SBATCH -o /fslhome/username/logfiles/dataset/output_temp.txt #SBATCH -e /fslhome/username/logfiles/dataset/error_temp.txt #SBATCH -J "ucsdtemp" #SBATCH --mail-user=LongbranchPennywhistle@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...
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Getting R Ready for Neuroimaging

There already exist some pretty good instructions on how to install ANTsR here . I still have had some people I work with ask me how to install it because sometimes it can be a bit quirky. So I’m briefly going over a way you can download it yourself. Note that ANTsR is currently only available for Mac and Linux. ANTsR has the following dependencies. mydeps <- c( "Rcpp", "tools", "methods", "magrittr" ) install.packages( pkgs = mydeps, dependencies = TRUE ) The packages listed here provide full functionality within ANTsR. You will need CMake to download it but if you don’t already have it there’s a CMake package that can be downloaded specifically for R on github. The traditional way to install ANTsR is to clone the packages from github and use the R CMD INSTALL <packagename> . However, sometimes it’s easier to not have to go back and forth between terminal and R’s interfac...
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