Chapter 13 DWI Preprocessing with Vistasoft

Unfortunately, the VistaSoft code is riddled with problems. Because the lab that originally has written the code is still running MATLAB r2012, newer versions or even different versions of MATLAB are going to have issues. Here are the changes you will need to make to your code in order for it to run correctly on helix:

vi ~/apps/matlab/vistasoft/mrDiffusion/dtiInit/dtiInit.m

Starting on line 163 (or maybe 170), we need to comment out one line of code. To comment out code in MATLAB, add a percent sign at the beginning of the command line:

% dtiCheckMotion(dwDir.ecFile,'off');

13.1 Job Script

On the remote computer create job script.

vi ~/scripts/ACAP/

Copy and paste.


#SBATCH --time=04:00:00   # 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

cd ~/scripts/ACAP/
module load matlab
module load lib/openblas/0.2.20-gnu
module load fsl/6.0.0
matlab -nodisplay -nojvm -nosplash -r "dtiVistaSoft('$1', '$2')"

13.2 Batch Script

First check that your subjid and ses are correct.

for i in $(find /work/ashley.ware/BIDS/ACAP/ -name "*b900_dwi.nii.gz"); do
  subjid=`echo $i | cut -d "/" -f6`
  ses=`echo $i | cut -d "/" -f7`
  echo $subjid
  echo $ses

If everything is correct then you can create your batch file.

Create script.

vi ~/scripts/ACAP/

Copy and paste.

curTime=`date +"%Y%m%d-%H%M%S"`
username=`id -un`
mkdir -p ~/logfiles/ACAP/${curTime}
for i in $(find /work/${username}/BIDS/ACAP/ -name "*b900_dwi.nii.gz"); do
  subjid=`echo $i | cut -d "/" -f6`
  ses=`echo $i | cut -d "/" -f7`
  mkdir -p /work/${username}/data/ACAP/dtiInit/${subjid}_${ses}
  sbatch \
  -o ~/logfiles/ACAP/${curTime}/output-${subjid}_${ses}.txt \
  -e ~/logfiles/ACAP/${curTime}/error-${subjid}_${ses}.txt \
  ~/scripts/ACAP/ \
  ${subjid} \
  sleep 1

13.3 MATLAB Function

The reason we are creating a function versus a script, is so we can pass a variable, namely the participant ID, into the script.

vi ~/scripts/ACAP/dtiVistaSoft.m

Copy and paste.

function dtiVistaSoft(subjid, ses)

% Display participant ID:

% Get home directory:
var = getenv('HOME');

% Add modules to MATLAB. Do not change the order of these programs:
SPM8Path = [var, '/apps/matlab/spm8'];
vistaPath = [var, '/apps/matlab/vistasoft'];
AFQPath = [var, '/apps/matlab/AFQ'];

% Set file names:
subjDir = ['/work/ashley.ware/BIDS/ACAP/', subjid, '/', ses, '/dwi/'];
dtiFile = [subjDir, subjid, '_', ses, '_acq-b900_dwi.nii.gz'];

% Don't change the following code:
ni = readFileNifti(dtiFile);
ni = niftiSetQto(ni, ni.sto_xyz);
writeFileNifti(ni, dtiFile);

dwParams = dtiInitParams();
dwParams.rotateBvecsWithCanXform = 1;
dwParams.phaseEncodeDir = 2;
dwParams.clobber = -1;
dwParams.outDir = ['/work/ashley.ware/data/ACAP/dtiInit/', subjid, '_', ses, '/'];
dwParams.dt6BaseName = 'dt';

% Here's the one line of code to do the DTI preprocessing:
dtiInit(dtiFile, 'MNI', dwParams);


13.4 Submit Jobs with Batch Script

Finally, submit the whole process by submitting the batch script.

sh ~/scripts/ACAP/

You can check the status of your jobs by checking if it is running or pending.


You can check the outputs.

tail -n 5 ~/logfiles/ACAP/<date>/output*

13.5 Download Directory / Sync Directory with Helix

Back on your local computer make sure you have the directory already.

mkdir -p /Volumes/bobo/data/ACAP/dtiInit

Then sync the data from the remote computer to your local computer.

rsync -rauv \ \