Hi,
figures out a few thing already by going through the source code.. pnm_evs.cc
I though I posted here, in case it may help others
>- when using the slice-time based regressors (RETROICOR, HR, and RVT), should you then turn off the slice-time correction in Feat pre-stats?
still not sure about this one, as it is not entirely clear how the slice-time correction in Feat is performed.
>- PNM slicetime option interleaved up/down: is 'interleaved up', the same as Interleaved in Feat, i.e. 0, 2, 4, 6 ... 1, 3, 5?
interleaved_up is indeed following the order of 0, 2, 4, 6,.... 1, 3, 5, but only for an odd number of total slices. For me this is the case
>- the PNM userguide refers to Chang 2009 et al, does this mean PNM also convolves the HR and RVT output with a cardiac and respiratory response function as described in Chang et al 2009 and Brin et al 2008?If not I guess I could convolve the output of PNM with the prescribed response functions my self per slice
Pnm doesn't perform any convolution with an response function form the literature. On default Pnm does heavily smooth the HR and RVT output tracs (10s, low pass filtering). To use literature response functions, best is to set the smoothing to 0s, and then perform the convulution with the response functions yourself. Also it is not really necessary to do the slice wise regressors for the HR and RVT as these vary very slowly wrt the slicetiming for BOLD fMRI
>- Does PNM also compute the respiratory varation metric (RV) as described in Chang 2009?
No it does not compute this one, I think RVT is probably just as good though and much easier to compute
best Jeroen
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