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Hi Anette, The problem with using radius of 0 was a bug. It's fixed in the attached version. Regarding the problem with sensitivity to the exact location it looks like it indeed has to do with MSP being very sparse solution so some vertices have very high values while others have low. So a difference of a mm in your location can result in some vertex either being included in the sphere or not and can make a big difference if that vertex has high activation. I can suggest 3 things you can try: 1) Use IID or COH instead of MSP. I tried IID and the results for -40 -18 7 and -41 -18 8 look very similar. 2) Try using MSP with the fine mesh. I haven't tried it but it might help as there will be more vertices to average over. In 10mm radius there are just 2-3 vertices with the 'normal' mesh. They probably have different orientations which might explain why some have very strong activation and some very weak. 3) Increase the radius even more until you see that the sensitivity to precise location goes away. Let me know if it helps. Best, Vladimir On Mon, Jan 30, 2012 at 7:38 AM, Anette Giani <[log in to unmask]> wrote: > Hi Vladimir, > > > > Sorry for that. Apparently I stopped the upload process to early. All files > should be available now. > > > > Best, > > Anette > > > > From: Vladimir Litvak [mailto:[log in to unmask]] > Sent: Friday, January 27, 2012 12:50 AM > To: Anette Giani > Subject: Re: [SPM] M/EEG: problems with sourcewave extraction > > > > Hi Anette, > > > > I also need the mat file from the mcMra... dataset. You only sent the .dat. > > > > Vladimir > > On Wed, Jan 18, 2012 at 7:47 PM, Vladimir Litvak <[log in to unmask]> > wrote: > > Dear Anette, > > > > The source data is not really helpful. I need the data you are extracting > sources from. You can send it via yousendit or dropbox. > > > > Vladimir > > > > On Wed, Jan 18, 2012 at 10:57 AM, Anette Giani > <[log in to unmask]> wrote: > > Thanks for the effort! > > Attached, I send you the script and the resulting .mat files. Sorry, I > cannot sen the original data, since it is too big. I hope that helps > already! Let me know if things are still unclear. > > Best, > Anette > > > > > On Tue, 17 Jan 2012 16:41:31 +0000 > Vladimir Litvak <[log in to unmask]> wrote: >> Dear Anette, >> >> I cannot reproduce these problems. It'd help if you send me your data and >> scripts or description of what you did exactly. >> >> Best, >> >> Vladimir >> >> On Tue, Jan 17, 2012 at 2:17 PM, Anette Giani >> <[log in to unmask] >> > wrote: >> > >> > Dear Vladimir,**** >> > >> > ** ** >> > >> > Thanks for your fast reply! I still have a couple of comments >> > though:**** >> > >> > ** ** > >> > >> > I think this is a result of summarizing over a sphere by extracting the >> > first eigenvariate. If you specify the radius as 0 you should get the >> > same > >> > thing you are getting in the plot.**** >> > >> > ** ** >> > >> > Specifying a radius of 0 gives an error:**** >> > >> > ** ** >> > >> > ??? Attempted to access XYZ(2,1); index out of bounds because**** >> > >> > size(XYZ)=[1,3].**** >> > >> > ** ** >> > >> > Error in ==> spm_eeg_inv_extract at 63**** >> > >> > dist = sqrt(sum([vert(:,1) - XYZ(i,1), ...**** >> > >> > ** ** >> > >> > Error in ==> Source_Extraction_Exp2 at 43**** >> > >> > Ds = spm_eeg_inv_extract(D);**** >> > >> > **** > >> > >> > Specifying a radius of 5 gives exactly the same results as in the gui, > >> > except that they are flipped.**** >> > >> > ** ** > >> > >> > Lastly, I would be great if you could advise what would be the most >> > reasonable approach to extract source waveforms from the primary >> > auditory >> > cortex? I would like to average across all vertices that lie within A1. >> > Is > >> > there a possibility to use an image mask to do so? **** >> > >> > **** > >> > >> > I think a simpler way would be to just specify some centroid for A1 and >> > radius large enough to include all of it. There is no resolution in >> > M/EEG >> > to make fine distinctions between A1 and the adjacent areas especially >> > when >> > A1 is strongly activated. So I don't think that using a mask will make a > >> > big difference. **** >> > >> > ** ** > >> > >> > I had the same idea. But results change a lot with respect to the ‘seed’ >> > region I take (i.e. [-40 -18 7] & [-41 -18 8]) and field intensities. >> > So > >> > how would you then decide on the seed region?**** >> > >> > ** ** >> > >> > Thanks a lot!**** >> > >> > Anette**** >> > >> > ** ** >> > >> > Best,**** >> > >> > ** ** >> > >> > Vladimir**** >> > >> > ** ** >> > >> > **** >> > >> > Looking forward to your suggestions.**** >> > >> > **** >> > >> > Anette**** >> > >> > **** >> > >> > **** >> > >> > ** ** >> > > > > >