Hi Colm,
How are you running that script, via tcsh or bash. I think they will be different. bash might pass the '\' characters to 3dDeconvolve, which will treat them as line separators for the GLT, meaning they would have different rows. For example, consider:
-gltsym 'SYM: 0.25*SpatialBranch +0.25*SpatialDelay +0.25*VerbalBranch \
+.25*VerbalDelay -.25*SpatialControl -.25*SpatialSwitch -.25*VerbalControl \
-.25*VerbalSwitch'
If 3dDeconvolve sees those '\' characters, this GLT would have 3 lines, each with its own Coef and Tstat, plus a final overall F for the 3 lines at once.
For example GLT#2_Coef would just be -.25*VerbalSwitch. You could easily verify that with 3dcalc.
Also, the text output from 3dDeconvolve should show the per-row glt's that come from the gltsym's. Those probably show multi-row tests.
Does that seem to be the case? And are you running this via bash?
- rick
