[Mne_analysis] Do I need to setup mri and do watershed etc procedure every time I re-analyze the data

[Mingbo Cai]

Dear colleagues,
Because recently I found some strange result while I did not compute signal-space projection(SSP) at the beginning, I decided to re-analyze the data with SSP. 

As my understanding from the Fig 3.1 of the manual (the workflow), the steps of mne_setup_mri, alignment, mne_watershed, mne_setup_forward_model are independent from the calculation of average and noise-covariance. On the other hand, it seems that only in the averaging and noise covariance steps I need to explicitly use the SSP, I thought I could do only the averaging and noise covariance calculation without the above steps, and use the bem and surface files generated in the last analysis to go on to mne_do_forward_solution and mne_do_inverse_operator. However, after I did these, in the mne_analyze interface, it did not allow me to view the source estimate on the surface (whenever I click on the timecourse manager window, it pops up to say "Surfaces do not match the source spaces. Cannot display estimates.") But when i click on the surface, the signal of that vertex can be displayed in the bottom-left window.

When I checked the log file of the outputs of the mne_do_forward_solution and mne_do_inverse_operator from the two times of analysis, it seems there are no difference except for the part of SSP and the SVD result due to that. All the correct files are used when I redo the analysis.

Does any one has a clue of what is the reason? And am I right that I do not need to redo those early steps if I only want to add SSP in my analysis?

Thanks very much 


Mingbo Cai
Department of Neuroscience
Baylor College of Medicine
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