The IDL program to calculate T₁, T₂, and r images requires two series of MRI images saved in BIN format.  The first series is the set of constant TR varying TE images, and the second series is the set of constant TE and varying TR images.  The filenames of the images and the imaging parameters and then recorded in a DAT file.  An example of such a DAT file is shown in the sample DAT file link.

    In the sample DAT file, the first number is the number of constant TR varying TE images (6 in this example), and the next number (1000) is the TR value (ms).  The next lines are the TE values (ms) followed by the image filenames.  The following line is the filename the user specifies for storage of the calculated T₂ image.  In this example, the calculated T₂ image was stored as a TIF file as the values were quite large.  The process is repeated for the constant TE and varying TR images.  The number of images (8) and the TE value (15 ms) is entered.  Then, the TR values (ms) followed by the image filenames are entered.  The next line is the filename the user specifies for storage of the calculated T₁ image, and the last line is the filename for the r image, both stored in BIN format for this example.
 

Running the code:
 

1. Open the program in IDL and compile.
2. Run the program either by typing "t1t2rhov5" at the command line or by clicking on the run icon.
3. The program prompts the user for the DAT file with the image filenames.  Select the DAT file.
4. The program prompts the user for the directory where the image files are stored.  Select a directory.
5. The program will ask the user whether to swap bytes or not.  If the user is not sure, make a selection and the program will open two images.  If the background in the image is not black, restart the program and make a different selection.
6. A box cursor will appear in the center of one of the two images opened.  Left click and move the box cursor with your mouse to a background region, typically the corner of the image.  Then right click to enter.  The program then finds the maximum value in the box cursor region and sets the noise level to that value.
7. Now, the program will calculate the T₁, T₂, and r images and store them under the filenames specified in the DAT file.  Run time is approximately 40 minutes total on a SUN UNIX workstation.