jist:CATNAP

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1 CATNAP (Coregistration, Adjustment, and Tensor-solving – a Nicely Automated Program)

CATNAP (Coregistration, Adjustment, and Tensor-solving – a Nicely Automated Program)

Here, we provide several layout files for duplicating the functionality in the original CATNAP program.
All tools used in these files have been released in open sourced on NITRC and are included with the default binary JIST distribution.
You may replicate this functionality exactly by placing modules from the JIST toolbox in your layout.

Prerequisites

JIST Pre-Beta 1.2 or Newer: http://www.nitrc.org/frs/?group_id=228
NOTE: For Pre-Beta 1.3 and below, use the .layout files from August 2009. For Beta 1.4 and above, use the layout files from October 2009.

DTI with Philips Par v3 Files

Sample Data Available Here: http://www.nitrc.org/frs/download.php/1009/020729.tar.gz Data use license: 'These data are freely available for research purposes. For publication, please identify the source of the data as "Data were obtained as courtesy of Dr. Mori (www.mristudio.org) in Johns Hopkins University."'
Download the CATNAP layout file: http://www.nitrc.org/frs/?group_id=228
Open the JIST Layout Tool and open the newly downloaded layout.

Create a text file that lists all PAR files to be processed together for each subject on one line. For example, if you acquired 3 repeated DTI scans for one subject and wanted to estimate a single tensor for each set of three scans, the text file would read:

/home/bennett/temp/01/020729/DTI/51/01_020729_51.par,/home/bennett/temp/01/020729/DTI/41/01_020729_41.par,/home/bennett/temp/01/020729/DTI/31/01_020729_31.par

Additional subjects should be listed on additional lines. Let's call this file pars.txt

Create a text file that lists all REC files to be processed together for each subject on one line. These files should be in the SAME order as the par files. For example, if you acquired 3 repeated DTI scans for one subject and wanted to estimate a single tensor for each set of three scans, the text file would read:

/home/bennett/temp/01/020729/DTI/51/01_020729_51.rec,/home/bennett/temp/01/020729/DTI/41/01_020729_41.rec,/home/bennett/temp/01/020729/DTI/31/01_020729_31.rec

Additional subjects should be listed on additional lines. Let's call this file recs.txt

In the layout tool, select the purple "Par Files" blob (1), click browse (2) for the list file, and (3) select pars.txt.

Repeat for the "Rec Files" blob, but select the recs.txt
Important: Inspect the fields of the "DTI Multi Gradient Table Creator". Some essential fields of the acquisition sequence are not included in the par file (for example fat shift direction). We have set this layout to use our default settings, but your settings may differ.
Select Project->Layout Preferences (1) and select an output directory (2). Optionally, adjust the maximum amount of memory or maximum number of simultaneous cores that will be run.

Save the layout file.
Open the JIST Process Manager (Project->Process Manager).

Verify that all modules are either "READY" or "NOT READY". If the status shows "FAILED" or "OUT-OF-SYNC", then you have selected an output directory that already contains processed results. You may remove these existing results at your own risk with Scheduler->Clean All.
When ready, click Scheduler->Start Scheduler.
- For more information on the process manager, see jist:ProcessManager
- For more information on the layout tool, see jist:LayoutTool

You may also run the layout from the command line. For example,

mipavjava edu.jhu.ece.iacl.jist.cli.runLayout ./CATNAP-PARv3.layout

- See the command line interface for more information: jist:CommandLineInterface
The result of running the above is a directory for each subject (exp-####) that contains a directory for each module (exp-####-A, exp-####-AB, etc.). These directories contain estimated tensor files, estimated contrasts, and a diffusion encoded color map.

UPDATE: July 2010

Here is a preview layout for using the new CATNAP with new PAR (v4.1+) files, which contain valid diffusion orientations.[1]

DTI with Philips Par v4 Files

Download the CATNAP layout file: http://www.nitrc.org/frs/?group_id=228
Processing with the Par-v4 layout file is identical to using the above par-v3 pipeline.
Important: Be sure to check the "DTI Multi Gradient Table Creator" settings for the protocol sequence. For example, the gradient table cannot be directly read from the par file.

DTI with Known Gradient Tables

If the gradient tables and b-values are known relative to the imaging volume, then it is not necessary to use the information in the PAR files to correct for slice angulation, patient positioning, etc.
The Par-v3 data above has .grad and .b value files. You may use this data as a test dataset.
Download the CANTAP layout for use without par files: http://www.nitrc.org/frs/?group_id=228
Open the layout in the JIST Layout Tool:

For each of the purple input blobs, "b0 Files" (1), "Grad Files" (2), and "Rec Files" (3), select the appropriate input file in the options box (4).
- b0 Files: This should point to a text file with one line per subject. Each line should contain a comma separated list of filenames. Each filename should point to a file that contains one b-value (in s/mm2) for each volume in the file.
- Grad Files: This should point to a text file with one line per subject. Each line should contain a comma separated list of filenames. Each filename should point to a file that contains a gradient direction for each volume in the file. The gradient directions should be normalized unit vectors. Either vertical or horizontal formatting is acceptable.
- Rec Files: This should point to a text file with one line per subject. Each line should contain a comma separated list of filenames. Each filename should point to one 3D volume or 4D series of diffusion weighted images.
- The volume and subject ordering in the above files must be the same for all three input fields.

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