How to Calculate T2 maps from a multi-echo series

What to do:

Type:

> T2Map -i infile.ext -o outfile.ext -f TE_File [t|V]

infile.ext: File containing the same image locations collected with the same tr, etc... at two or more different te's. The file order is assumed to be constructed of all locations at the first te, followed by all locations at the second te, etc...
outfile.ext: Desired output file. This name must end in .bfloat or .img, as the output data type must be floating point.
The output file will contain four images: 1) spatial map of T2 values 2) map of M0 (te=0) 3) map of chi² values 4) R2 map (1/T2).
This program performs inline type conversion. The output type is determined from the output file name.
TE_File: Text file containing the values of te that correspond to each image in infile.ext

**Options**
-t	If this option is included, only points with values above the number that follows will be used in the analysis. Otherwise, the threshold is calculated from the image data themselves. If -t 0 is entered, there will be no thresholding, and all data points will be included.
-V	Verbose output

The full source for T2Map can be found [HERE]

This page is maintained by Mark Cohen [updated 5.20.06]