I think I found the answer to my question 1 - in case it is helpful for others. On a Mac I am running, from a Terminal window (the Mac Terminal, not Sdm):

/Applications/SdmPsiGui-osx-v6.21/SdmPsiGui.app/Contents/Resources/bin/osx/imgcalc mymap.nii.gz -set_mni
/Applications/SdmPsiGui-osx-v6.21/SdmPsiGui.app/Contents/Resources/bin/osx/imgcalc mymap.nii.gz -set_t [dof]

RE question 2, I tried not to include the t_thr column, but then I couldn't start the preprocessing. In the log indeed it says WARNING: Row 't_thr' not found in the table.. The program will close as this problem could cause fatal errors. So I have included it, but left it blank. Does this make a difference, compared to fill it with NA?

I would also still appreciate answer to questions 3 and 4, in particular getting a blank page (sometimes completely blank, sometimes with headers and ?? like in the screenshot) when opening the z_tfceCorrected_p_0.02500_1.htm file.

Could you also confirm whether I am correct in using FSL Raw test statistic from randomise as input (_tstat)?

Thanks so much in advance.