TORTOISE on the Biowulf Linux CLuster

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TORTOISE on Biowulf

TORTOISE (Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble) is for processing diffusion MRI data, and it contains two main modules, DIFF_PREP and DIFF_CALC.:

DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space
DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis

DIFF_CALC is GUI-based. DIFF_PREP has a command-line option and can be used on Biowulf for multiple simultaneous runs. This procedure is described below.

Tortoise was developed at NICHD, NIH. TORTOISE website

Tortoise requires IDL. There are 20 IDL licenses on Biowulf/Helix. Each IDL run requires 6 licenses. Thus, it is only possible to run 3 total instances of IDL on Biowulf. (multiple Tortoise/IDL processes on a single node count as a single IDL run for licensing purposes).

It is most advantageous to run Tortoise/IDL on nodes with the maximum number of cores. As of Jan 2012, these are the 24-core x2800 nodes.

Process several subjects using Tortoise/IDL

(Sample scripts and procedure courtesy of Vivek Buch, NINDS)

1. For each subject, the raw diffusion-weighted MRI images in DICOM format, DTI_proc directory (created by the "import" process in the DIFF_PREP GUI), and the subject's high resolution structural image (e.g. T1 or T2 image, but recommended image is a T2 with fat sat) need to be transferred to Helix/Biowulf into a unique directory, e.g. for SUBJECT1, the directories could be

/data/user/SUBJECT1/scan1/DTI_proc                        (DTI_proc dir)
/data/user/SUBJECT1/scan1/highresstruct_image.nii         (T2 image)
/data/user/SUBJECT1/scan1/DTI                             (raw DWI images)

Each subject scan must have an "xml" file that directs TORTOISE to the DTI_proc and the high resolution structural image within this subject and scan directory. The xml file can be stored anywhere on biowulf (/home/user/myXMLfiles or /data/user), it does not have to be in the same folder as the subject's data. Information on this xml file is on the Tortoise website. This subject scan-specific xml file will be the input into diffprep.

2. Set up a script along the following lines. This script can be used for all future runs and will not need to be changed.

-------------------------file diffprep.sh--------------------------------
#!/bin/bash

cd /usr/local/TORTOISE/DIFF_PREP/diffprep_main

idl <<EOF
diffprep,$1
EOF

3. Set up a batch script along the following lines. This sample script includes 4 subject scans, but if submitting to a 24-core node, up to 24 subject scans can be included in a single batch file. The input parameter for the diffprep.sh script is the XML file described above.

Note: The spaces, non-spaces, single quotes, and double quotes are required exactly in this format.

----------------------- file tortoise.bat --------------------------------
#!/bin/bash
#PBS -N TORTOISE                           #name of job
#PBS -V	                                   #export environment -- NECESSARY!
#PBS -m be                                 #send email at beginning and end of job

#
cd /home/user/myscripts                   #location of the diffprep.sh script

./diffprep.sh "'/home/user/myXMLfiles/SUBJECT1-scan1.xml'" &
./diffprep.sh "'/home/user/myXMLfiles/SUBJECT1-scan2.xml'" &
./diffprep.sh "'/home/user/myXMLfiles/SUBJECT2-scan1.xml'" &
./diffprep.sh "'/home/user/myXMLfiles/SUBJECT3-scan1.xml'" &
wait

4. Submit this job with:

qsub -V -l nodes=1:c24 ./tortoise.bat

This job will be submitted to a single node with 24 cores, and will use 6 IDL licenses.

If Tortoise runs successfully, the DTI_proc directories will be updated with new files tagged by "_DMC_" which means distortion motion corrected. If it does not work, the DTI_proc will not have any files with this tag. Users can check for the existence of these files to see if the run was successful.

Documentation

TORTOISE website.