Quick start & fitting for T2

  1. Create a separate directory to hold the contents of the FIT analysis. This isn't a requirement, but you will find that this simplifies location and identification of files. Sometimes you may want to have several related fits, with each grouped in its own directory.

  1. This FIT analysis requires one top level "control file" that specifies various options and also lists the scans (data files) to be fit. Refer to the sidebar for an example.

  1. Some fits (e.g., T1 or T2) require no additional files. The array of echo times (for T2 fits) or inversion times (for T1 fits) is specified by the “x-array” in the fields prior to the list of scans/files. Other fits (e.g., DTI) have more complicated input and thus require a description file for each data file.

  1. Run the fit program for all voxels by using the simple command

fit fit.dat

     where “fit.dat" is the name of the control file in this case.

  1. Display the time series and all maps using jip-display (a.k.a, xd):

"xd -t fit.dat &"  or  "xd &”   (see below)

  1. When “fit" was executed in step 4, it created a hidden file named ".display" with default contents "xd -t fit.dat". If no arguments are given to "xd", and if this file exists on the current directory, then the arguments within the file will be used. This is why one can type simply "xd" in step 5. Consider modifying file ".display" using an editor to include whatever arguments are useful. Then, when you revisit this directory many months later, you can simply type "xd" to bring up the analysis. Example:

xd -t fit.dat -e /space/1/me/template/anatomy.nii -o /space/1/me/template/overlay-list.dat

Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard