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Quite clear now. Thank you very much for the explanation. Best regards, Carlos On 18/02/2008, Mark Jenkinson <[log in to unmask]> wrote: > > Hi, > > This is actually a relatively subtle issue. > > You can set the GLM up to work like this (explicit baseline) and have > it be > consistent, as long as the mean value of the signal contains useful > information. > However, in FMRI this is not the case and that is where the complication > comes from. > > Since the mean value of the FMRI signal is not useful, it either > needs to be > removed from the EVs and data by demeaning (which is what FEAT does) > or included as a nuisance regressor in the GLM. Either way, it is > then not > allowable in the GLM to have any combination of the remaining EVs which > add up to a constant signal (which would be equivalent of modeling > the mean > a second time). Doing this would make the design rank deficient. > > So consider an experiment with one type of stimulation. If you have > one EV > for activation and one EV for baseline then each timepoint will > either be > part of the activation EV or baseline EV. If there was no HRF then > this would > be totally rank deficient as the addition of these two EVs would be > equal to > a constant for all timepoints. However, the HRF delays and blurs to > some > extent which means that the ends of the timeseries don't quite end up > being > a constant (but are close) and so the model is nearly rank deficient, > although > technically you can results from it - they are just poor results. > > The situation is equivalent for more than one stimulation, as the sum > of all > the EVs typically adds up to a constant. > > The bottom line is that in practice the baseline needs to be left as > implicit, > and not explicitly modeled, due to these rank deficiency issues, > which are > a consequence of the fact that the mean signal contains no useful > information > and is removed. In FEAT the mean is removed automatically, so you do > not > see this typically, although Featquery does use the mean value when > calculating percent signal change. > > I hope that all this helps explain why things are as they are. > > All the best, > Mark > > > > > On 15 Feb 2008, at 18:42, carlos silva pereira wrote: > > > I get it, it's quite logical to ignore the baseline when > > contrasting 2 EVs. > > Still it seems the same as considering the baseline an EV and then > > doing EV1-EV2 (baseline) and not the 1 0 0 contrasts. > > But I may be missing the point... > > Best, > > Carlos > > > > > > On 15/02/2008, Mark Jenkinson <[log in to unmask]> wrote: Hi, > > > > If you do a difference between two EVs in your contrast then it > > doesn't matter. > > It is like doing (effect1 - baseline) - (effect2 - baseline) = > > (effect1 - effect2) > > > > Note that this is true for any contrast that adds up to zero. > > > > So in contrasts like that the baseline is irrelevant. > > > > But in the simple "1 0 0 ..." type of contrasts it obviously is > > important and you are > > looking at effect1 wrt baseline. > > > > All the best, > > Mark > > > > > > On 15 Feb 2008, at 18:23, carlos silva pereira wrote: > > > > > Thanks for the quick reply! > > > One last thing: when I specify a contrast between two EVs, will > > > they be previously contrasted to the baseline to? > > > For example: in contrast1 I define a value of 1 for EV1 and in > > > contrast2 I define 1 for EV1 and -1 for EV2. > > > In contrast2 will EV1 and EV2 be contrasted to baseline also or > > > just to each other? > > > Thanks again, this forum is a major help for starters! > > > Carlos > > > > > > On 15/02/2008, Mark Jenkinson <[log in to unmask]> wrote: Hi, > > > > > > You should not use baseline EVs in Feat. > > > It may work, but it will be close to rank deficient normally. > > > The best way is to omit it and then all EVs are implicitly > > contrasted > > > wrt baseline and the modeling inside Feat works optimally. > > > > > > All the best, > > > Mark > > > > > > > > > > > > On 15 Feb 2008, at 18:10, carlos silva pereira wrote: > > > > > > > Hi to all! > > > > Basic question: in the Feat full model setup is it the same to 1) > > > > consider the baseline condition as en EV and contrast it with the > > > > main condition; 2) just omit the baseline and FSL will contrast it > > > > with all the EV's? > > > > I ask this because I tried both options and results are very > > > > similar, although not absolutely equal. > > > > Thanks in advance. > > > > Carlos > > > > > >