just to be sure, i followed your example from the suma usage page:

3dWarp –matvec_in2out example_func2highres.mat –fsl_matvec –gridset ExpVol+orig –prefix Func2 stats/zstat2.hdr

shouldn't this properly handle fsl type .mat files?

so, i ran this command:

3dWarp -matvec_in2out anat015acup2MNI.mat -fsl_matvec -gridset avg152T1+orig -prefix test0153dwarpfslmatvec anat015acup_0000.hdr

the test0153dwarpfslmatvec+orig dataset was not aligned.

but... running with flirt produced an aligned output dataset:

flirt -in anat015acup_0000.hdr -ref avg152T1_brain1_0000.hdr -applyxfm -init anat015acup2MNI.mat -out test015flirt


-vitaly