- 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
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.
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
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