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Hi, Thank you for the helpful response and the code for the % variance, much appreciated. I agree that the threshold is arbitrary but I would still say it is necessary - if I used unthresholded (or thresholded at P=1.0) to define my subject-level peak (for centre of the VOI), I might expect a high chance of that peak being a spike or other artifact. Bw, Liam ________________________________________ From: Zeidman, Peter [[log in to unmask]] Sent: 28 March 2014 11:47 To: Mason, Liam; [log in to unmask] Subject: RE: VOI thresholding queries Hi Liam, You're choosing the voxels to include for individual subjects' ROIs, but I think you're saying your inference will be at the group level. In which case, common practice is to just take all the voxels at the individual level corresponding to the group cluster, or alternatively, create single-subject rois (e.g. spheres) which vary in their centroid up to a fixed maximum distance from the group peak. As for excluding some voxels, e.g. using a t-statistic equivalent to p < 0.5 or p < 0.1, my personal opinion is this is quite arbitrary, as you would not necessarily expect a voxel to have significant activation at the single subject level, even if it's part of the group peak. Others may have different opinions on this... Best, Peter. > -----Original Message----- > From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] > On Behalf Of Mason, Liam > Sent: 28 March 2014 11:34 > To: [log in to unmask] > Subject: Re: [SPM] VOI thresholding queries > > Hi, > > My question refers to selecting VOIs at single subject level, that lie > near to a set of co-ordinates already identified at group level. I also > constrain this within an anatomical structure. > > Any further input from the list greatly appreciated. > > Thanks, > Liam > > ________________________________________ > From: Zeidman, Peter [[log in to unmask]] > Sent: 28 March 2014 09:54 > To: Mason, Liam; [log in to unmask] > Subject: RE: VOI thresholding queries > > Hi Liam, > Could you clarify whether you want to make inferences at the single > subject or group level? And how is your ROI defined - is it based on a > group activation? Or single subject activation? Or anatomical > structure? > > Note that if you're making inferences at the group level, you would not > necessarily expect significance at the single subject level. > > The variance explained gives you a sense of how much of the signal you > have captured in your principle component (ROI) - it might be that you > are perfectly modelling 5% of the signal, but there are more > substantial processes going on that are not included. You'll generally > find it varies as a function of the size of your ROI. It's shown in the > GUI, but I'm not sure if it's stored. > > Best, > Peter. > > > -----Original Message----- > > From: SPM (Statistical Parametric Mapping) > [mailto:[log in to unmask]] > > On Behalf Of Mason, Liam > > Sent: 27 March 2014 15:14 > > To: [log in to unmask] > > Subject: [SPM] FW: VOI thresholding queries > > > > Hi there, > > > > Can anyone help with the following VOI queries? > > > > First, I am having difficulty deciding on a threshold for individual > > subject VOI - is there a trade-off in terms of 'quantity' (number of > > voxels included) and their 'quality'? Where poor quality might mean > > including voxels with spurious or artifactual activations. > > Practicaly, thresholding with P=.1 fails to find any voxels for a > > substantial number of subjects, so I will need to relax this. P=.5 > (or > > even P=1) is commonly used but seems too relaxed(?) For subjects > where > > a robust/non-artifactual peak is identified at e.g. P=.1, won't > > dropping this threshold further increase the chance of finding an > > artifactual peak? > > > > Second, is the amount of variance explained by the VOI a good > measure > > of 'quality'? In which variable would this value be stored for each > > subject (can't find it in any of the fields of xY returned by > > spm_regions function) > > > > Any help would be much appreciated! > > > > Many thanks, > > Liam