startup & output

jip-srtm (aka srtm) is designed as a unix/linux program that requires that all necessary files are specified on the unix line at startup.  The general syntax is

srtm  [GLM control file]  [options]                             example: srtm srtm.dat

This program has few startup options (below).


Other input options

-h or -H        Get help, either the short version (-h) or the long version (-H).

-v or -V        Use verbose output.

-t [ID]           Calculate the best value of the washout time constant for the reference region (tau2_ref) using an error-weighted average of 

                    values computed across all voxels in the target region. The “ID” specifies the event name in the GLM model; an event with that

                    ID must exist in the GLM model and have type “k2”.

-T [ID]          Calculate the optimal value of the time constant for a gamma or sigmoidal k2a term that models displacement. 

                    Test both gamma and sigmoidal functional forms, as well as a shaped gamma function with a non-unity alpha shape parameter.

                    The ID specifies the event name in the GLM model; an event with that ID must exist in the GLM model and have type “k2a”.


Output files

For each condition specified in the GLM control file, there will be 3 output files:

  1. P-value maps                      P-condition.nii               e.g., P-A.nii
  2. T statistic maps                   T-condition.nii               e.g., T-1.nii
  3. Signal change maps            S-condition.nii               e.g., S-a.nii
  4. Binding potential maps        BP-condition.nii             e.g., BP-A.nii


                                                       Display

After running the program as above, display using jip-display from the same directory. You may want to add options to the “.display” file.

xd &


Time-activity curve from a single voxel in basal baglia showing displacement (purple line, with gray error bars).

Yellow points = data, white line = total fit, green & red lines = components of fit.

Values of parameters and conditions are evaluate for single voxels or ROIs.

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