Required files

Three types of files are required to run this executable:

  1. A control file at the top level; generally these files are called something like “glm.dat” or “srtm.dat”;
  2. One file per scan that describes the scan parameters; generally these files use a “.glm” extension;
  3. One table file per scan that includes the frame times and optionally other columns.

SRTM Control File

At the top level sits the main file that follows a format similar to all other time models in jip software. The format of this file is specified in detail here.

GLM files

For each scan, use a text editor to create a description of the file in terms of the parameters to be used in the GLM analysis of the SRTM model. The general structure mimics the format used for fMRI files. Namely, GLM parameters are identified by a single character (1-9, a-z, A-Z) so that a condition for adding A+B-C-D would be denoted as “AB-CD”. The basic form for each parameter identification line is

 [parameter ID] [type (R1, k2, or k2a)] [shape (constant, gamma, sigmoid, table)] [optional shape parameters]

Following this line, one in principle can specify a number of periods by denoting on and off times for constant shapes, or multiple instances of other shapes. Blank lines indicate that a new parameter will follow. By default, the shape is constant, so that one can write “1 R1” rather than “1 R1 constant” . By default, the start and stop times span the run, so that one can leave out this information as well.

   The shapes “gamma” and “sigmoid” require a time constant to define the shape. The “gamma” function can take one additional parameter (alpha) to define the shape as (t/tau)^alpha*exp(alpha*(1-t/tau):

      A k2a gamma 10 .5   # parameter “A” is a k2a parameter with time-to-peak 10 min and is flattened

Finally, one can exclude regions from analysis using the keyword “exclude”:

      exclude 80,90-n

Table files

For each scan, create a  text file with 1) a single row of column headers at the top, and 2) one entry in each column for each time frame in the PET data file. The total number of rows in file should equal the number of time frames plus one extra for the header. The first column is always required to be the length of PET frames in units of seconds. Other columns are optional and rarely used. The only reason for other columns is to enable the user to specify a user-defined shape for one of the GLM parameters.

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