Dear experts,

I am using SDM to conduct an IBMA with unthresholded statistical maps and I have a few questions for which I would really appreciate your help.
1. According to the tutorial, I need to convert the images first, using the [Convert images] button. Using the button, I have to manually select each image and enter the DoF. I have several maps and I need to run several analyses, is there a way to use the command line to complete this step, rather than doing it manually?
2. Because I have statistical maps, I don't have t-value thresholds. Should I still include a t_thr column, and filled it with NA?
3. The FWE correction/permutation step takes quite a long time. As mentioned before, I have several analyses to run, so I was wondering if there is a way to run the analyses in parallel?

Thank you very much in advance!

Elena

Sorry, I also have another question. If after running FWE correction and threshold I get a blank html page, only with the titles (see attachment), does this mean there are no significant results?

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.

Dear Elena, 

Sorry for the late response. and I'm happy you get answers to some of your questions

For SDM, a empty column for the t_thr is the same as fillinf it with NA, so it's the same.

Indeed, if you get an empty webpage is that there is no significant results for the contrast/threshold you set.

You can use the randomise tstat as input for the t-images in SDM. 

The only way to make FWE faster is adding more CPUs in the prompt, but there is nothing else to do

Best, 
Lydia

Thanks so much for taking the time to respond Lydia!