Calculate T2*

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T2StarScreen.JPG

Algorithm Description

To calculate T2* using multi-echo gradient sequence images. This program also computes the error in T2* given the error in the original signal. See attached document for details on the formula used.

Calculate T2* Input

Noise (Mean) - Mean of the noise. In order to estimate this value, open the image set you are about to use and scroll to an image about mid-way through the set of slices. Select a region outside of the core image region of interest. View the histogram of the region. Find the pixel strength on the tail end where the number of pixels with that stregnth is very small. Divide that number by 3. The program reduces all pixels with signal strength less than 3 times the noise signal to 0.

Initial Std. Deviation for the Image - This is the sigma0 used in the calculation of the error in T2*. See the attached document (see formula (4)) for more details. In order to estimate this value, open the image set you are about to use and scroll to an image about mid-way through the set of slices. Select a region of interest (not the noise). View the histogram of the region. Approximate this value based on sigma value displayed on the histogram.

Dr Haacke told me that another way to estimate this is to select the noise region and take the mean value and then multiply that by 0.8.

TE Sequence File(s) - Select two or more echo image set. The program uses linear least square fit algorithm to compute the T2*. It uses the same formula for two echo image set as well as case where there are more than two echo images.

In order to select the first echo, click the "Browse" button. Browse to the folder containing the first echo and select the first slice. If the file format is DICOM, the program will automatically read the Echo Time (TE) from the file. If the image format is not DICOM, enter the Echo Time in the text box below the main file name text box, Click the "Add >>" button to add the image. The image name will be added to the list box below.

Follow the same steps to add more echos.

If you want to remove any echo, click on the image name in th list box and click "Remove <<" button. The image name will be deleted from the list.

You can select the echos in any order you like. The program sorts the echos in increasing echo time order before using them in the calculation.

Calculate T2* Output

T2* images are produced and stored in the folder you choose in the Input Dialogue.

Output Folder and Prefix - Click the "Browse" button and select the folder where you want to save the output T2* images. Provide just the prefix you want to use for the image name. The images are saved as prefix-1.ima, prefix-2.ima, and so on.

Specify the values where you want the T2* values outside of that bound set to a specific value. By default all values outside the range of 0 and 250 is set to 0.

Location