$Id: README,v 1.4 2007/07/13 03:26:56 greve Exp $

These are diffusion gradient direction files that describe some of the
protocols distributed by Siemens though the MGH DTI Sequence Package.
These are used at the Massachusetts General Hosptial (MGH) Martinos
Center for Biomedical Imaging as supplied by Thomas Benner. The
sequence names usually start with "ep_b". If you do not have or are
not using the MGH DTI Sequence Package, then these files will not be
of use to you.

DISCLAIMER: THERE IS NO GUARANTEE THAT THESE ARE THE GRADIENTS THAT
WERE USED IN YOUR ACQUISITION. MAKE SURE YOU KNOW WHAT YOU ARE
DOING!!! 

IF YOU ARE USING VB13 OR HIGHER, THEN THE TABLES FOR THESE NUMBER OF
DIRECTIONS WILL BE INVALID: 6, 10, 12, 20, 30, 64, 256. Siemens uses
their own internal tables tables for these numbers. VB13 is supposed
to include the gradient directions in the header (but I have not been
able to find them yet).

The files are named according to the following format:

   gradient_mgh_dtiNN.gdt

where NN is the two-digit, zero-padded number of directions (eg, 06
for 6 directions or 72 for 72 directions). 

Each file will have three columns with the number of rows equal to the
number of directions. Each row is a gradient direction of unit length.
The directions are in the magnet frame.

The file does not indicate the bvalue or the number of acquisitions
for which the bvalue is 0. These can be obtained in one of two ways:

1. From a private field the Siemens dicom file (or an "infodump" file
created by unpacksdcmdir or mri_probedicom).

The relevant fields are:

sDiffusion.alBValue[1] = 700 [Indicates the bvalue]
sDiffusion.lDiffDirections = 60 [Number of diffusion gradients]
sWiPMemBlock.alFree[6] = 60 [Number of diffusion gradients, redundant]
sWiPMemBlock.alFree[8] = 10 [Number of images in which bvalue=0]

These can be found by running the unix 'strings' program on the dicom
file. Note that all the relevant information can be obtained from one
dicom file. It will usually be assumed that the bvalue=0 images will 
be acquired first.

2. Examining the pulse sequence name in each dicom file. This is
stored in the (non-private) dicom tag (18,24). The sequence name will
have the following format:

  ep_bX#N
    X = bvalue
    N = nth acq for that bvalue

So, if you have 5 acqs at bvalue=0 followed by 6 with bvalue = 700:

  ep_b0#0
  ep_b0#1
  ep_b0#2
  ep_b0#3
  ep_b0#4
  ep_b700#0 --> N restarts at 0
  ep_b700#1
  ep_b700#2
  ep_b700#3
  ep_b700#4
  ep_b700#6

Note that all the dicom files in the series need to be queried in
order to obtain all the relevant information.