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What does your mask look like? Also, what does the zstat1.nii.gz file look like? -- David V. Smith Graduate Student, Huettel Lab Department of Psychology and Neuroscience Duke University Durham, NC 27708 http://www.mind.duke.edu/huettellab/ On Dec 8, 2009, at 11:20 AM, Shal Hat wrote: > Regarding my previous message: > Just to clarify, Am talking about ME group analysis that did not provide any activation. The first level and and FE provided relevant activation. > I tried OLS, FLAME1, and FLAME1+2, and no activation in all these ME algorithms. Also, the full model setup was a group mean where all the inputs were set to 1.0. > > Thanks, > > > > On Tue, Dec 8, 2009 at 11:09 AM, Shal Hat <[log in to unmask]> wrote: > I corrected all the registration problems did a first-level followed by a FE, and then cross subject ME _FLAME1. However > even with a p value of 1 ! there was no activation. The cope was fixation against a visual sitmulus. I should at least see something, not > 0 activation. > > > On Thu, Nov 26, 2009 at 10:07 PM, David V. Smith <[log in to unmask]> wrote: > Try using the cope images from the second level as the input. Select "Inputs are 3D cope images" in the data tab (the input should be something like this for cope 1: subject.gfeat/cope1.feat/stats/cope1.nii.gz). You'll do a group-level ME analysis on each cope of interest. > > > > On Nov 26, 2009, at 9:59 PM, Shal Hat wrote: > >> Am not sure if the activations are very consistent across the sessions. However some show some consistency. >> Also, I have seen some recommendations to put the p value around 1. However, am a bit concerned about that recommendation. >> Am currently trying to run FLAME 1 on the FE results but am getting an error stating that the feat directories do not contain any >> reg data. This is although the reg. was successfully done for all the first level analysis and worked fine with FE, but now am getting >> the error for ME. >> >> Thanks again,, >> >> On Thu, Nov 26, 2009 at 6:17 PM, David V. Smith <[log in to unmask]> wrote: >> If you're seeing consistent activations across all your runs in a given subject, but not seeing anything for that same subject's FE analysis at the 2nd level, I would be a little surprised. Is that what is happening? You can try making the threshold a little less conservative at the 2nd level, if you just want to be sure everything is working, but I would run the ME group analysis with whatever threshold you're comfortable using in a paper. >> >> Cheers, >> David >> >> >> >> On Nov 26, 2009, at 3:59 PM, Shal Hat wrote: >> >>> Thanks David, >>> >>> I resolved the issue of correlated EVs. That is not an issue anymore. >>> Am actually seeing some activations at the first level, but not at the FE higher level for each respective subject. >>> >>> So, would you recommend moving on to ME group analysis before going back and increasing the threshold? >>> >>> Thanks,, >>> >>> On Thu, Nov 26, 2009 at 1:21 PM, David V. Smith <[log in to unmask]> wrote: >>> The first thing to note is the statistical thresholds that you utilize at each level are independent -- the second and third level analyses only care about the copes and the varcopes from the preceding analysis. >>> >>> That said, your thresholds might be a little conservative (although "correct" as Jesper pointed out earlier). If your maps are blank at the first and second levels, I personally wouldn't worry too much about it because it's difficult to see robust effects at these stages unless you have a lot of power. In your case, however, you might be suffering from the correlation between your EVs. Run the third level analysis and see if your results make sense. >>> >>> David >>> >>> >>> >>> >>> On Nov 26, 2009, at 11:46 AM, Shal Hat wrote: >>> >>>> So, this is what I did: >>>> >>>> 1) First level analysis for each of the 5 runs for each subject with z>2.3 and p<.0125 (.05/4 contrasts) >>>> 2) Higher level FE analysis of the 5 runs for each subject. >>>> 3) I haven't done this, but plan to: FLAME ME for all subjects. >>>> >>>> Up to number 2 above, I am not seeing any activation. My question is, am I being too conservative with my z >>>> and p-value thresholds? Any suggestions regarding these values in this context? >>>> >>>> Thanks !!! >>>> >>>> >>>> >>>> On Sun, Nov 22, 2009 at 2:17 PM, Shal Hat <[log in to unmask]> wrote: >>>> I'm pretty sure I haven't. However, from what I read, I understood that the SVD algorithm used is very conservative. >>>> Also,it is worth noting that the diagonal on the matrix has a few dark squares (0.000). >>>> >>>> >>>> >>>> On Sun, Nov 22, 2009 at 11:12 AM, David V. Smith <[log in to unmask]> wrote: >>>> I don't think that error has anything to do with your contrasts. Your EVs must be highly correlated. Perhaps you mistakenly entered the same EV twice? >>>> >>>> >>>> On Nov 20, 2009, at 5:24 PM, Shal Hat wrote: >>>> >>>>> I am in the process of analyzing each run/subject with 6 EVs. However am getting the common rank deficient error. I am assuming this is >>>>> most probably due to the many contrasts. Is there a way around this. >>>>> >>>>> To reiterate my scanning protocol, I have five acquisitions per subject. >>>>> In essence, it is one stimuli split across the 5 scanning sessions, and I currently have 6 EV. Actually I have more, but 6 will do for now. >>>>> >>>>> Thanks ! >>>>> >>>>> On Thu, Nov 12, 2009 at 6:03 PM, Jesper Andersson <[log in to unmask]> wrote: >>>>> Hi again Dav, >>>>> >>>>> >>>>> The one thing that still seems to be a bit of an issue is whether I can correct for multiple contrasts, for example, if I have 1 contrast of interest, or 2 or 100 (in theory only!). If I do higher-level contrasts independently for just 1 contrast vs. 100, I am nearly guaranteed to get spurious significance in the latter case. In my case, I have a handful of contrasts (which are actually largely independent - along the lines of modelling 3 two-level factors and the interactions between them). Thus, I am still a little concerned about correcting for these multiple (but at least partially independent) contrasts. >>>>> >>>>> Or is this handled already by those contrasts having been specified simultaneously at the first two levels? >>>>> >>>>> this is something that is, funnily enough, largely ignored in neuroimaging. If you ask a question through some contrast and threshold the resulting SPM at a FWE-rate (i.e. corrected for multiple comparisons among the voxels in that SPM) of 0.05 you basically say that you accept 1 false positive out of every 20 times you test a contrast. >>>>> >>>>> If you use two different contrasts in the same data the false positive rate pretty much doubles, for the experiment as a whole. And so it goes as you keep coming up with more contrasts. >>>>> >>>>> So you are right that in your average neuroimaging paper the false positive rate is typically much higher than 0.05, for the paper/study as a whole. >>>>> >>>>> This is very easy for you to "fix" yourself. Let's say you are doing a study where you want to test four different contrasts. Test them at a 0.05/4 FWE level instead, and you will have a false positive rate of 0.05 for your paper/study. >>>>> >>>>> Chances are you'll report fewer blobs though ;-) >>>>> >>>>> Good luck Jesper >>>>> >>>> >>>> >>>> >>> >>> >> >> > > >