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”.
For each condition specified in the GLM control file, there will be 3 output files:
- P-value maps P-condition.nii e.g., P-A.nii
- T statistic maps T-condition.nii e.g., T-1.nii
- Signal change maps S-condition.nii e.g., S-a.nii
- Binding potential maps BP-condition.nii e.g., BP-A.nii
After running the program as above, display using jip-display from the same directory. You may want to add options to the “.display” file.
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.