depends on what you are getting the direction of the result for and how you want to interpret it. If the cluster has both pos and neg, then the interpretation becomes more difficult. Is this really happening? I don't think I've ever seen it. The abs() just takes the absolute value, there is no summing across the cluster, just counting voxel above threshold. If you really want to evaluate the sign, you can do a signed test (corrections across signed and unsigned tests then become problematic). Finally, the 1.3 threshold is way to low when using the MC-Z simulation. If you want to use a threshold that low, then you'll need to use a permutation instead. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 05/14/2018 06:33 PM, Pedro Rosa wrote: > > > Many thanks, Doug! > Should I then rely on groups' means to determine the 'direction of the > result', and not on the 'max statistical significance' signal? > Does 'abs' simulation sum up the results I could get by running 'pos' > and 'neg' simulations separately? > Best > > On Mon, May 14, 2018 at 7:13 PM, Douglas N. Greve > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > You have specified "abs" meaning an unsigned "absolute" test, so > there > is no guarantee that the mean contrast will be pos or neg. > > > On 05/14/2018 06:11 PM, Pedro Rosa wrote: > > > > > > Here it is: mri_glmfit-sim --glmdir > > PEP-HC_Gender_Age.txt.lh.area.mgh.5.mgh.cortex.glmdir --sim-sign > abs > > --cache 1.3 abs > > > > On Mon, May 14, 2018 at 6:59 PM, Douglas N. Greve > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>> > wrote: > > > > sorry, one more thing. Can you send your mri_glmfit-sim > command line? > > > > > > On 05/14/2018 05:46 PM, Pedro Rosa wrote: > > > > > > > > > Hi, Doug. Many thanks. > > > Find the fsgd and the contrast attached, as well as the > cluster > > > summary and the individual-based cluster data (which I used to > > > calculate the groups' means). The cluster I referred to is the > > second > > > one (medialorbitofrontal). > > > I investigated differences in cortical area from groups 1 > and 2 in > > > contrast to groups 3 and 4 (contrast 3 as in > > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V> > > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V > <https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V>>). > > > Best, > > > Pedro Rosa. > > > > > > On Mon, May 14, 2018 at 5:42 PM, Douglas N. Greve > > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> > > <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>>>> > > wrote: > > > > > > Can you send your fsgd file and contrasts? > > > > > > > > > On 05/14/2018 01:25 PM, Pedro Rosa wrote: > > > > > > > > > > > > Dear FreeSurfers, > > > > I got results from a cortical area analysis that > intrigued > > me: Upon > > > > the inspection of clusters that survived Monte-Carlo > > simulation, I > > > > found a cluster with larger area among a first group in > > contrast > > > to a > > > > second group. > > > > However, when I calculated the cortical areas means > from that > > > cluster > > > > (as available in the glmdir), the second group had > values > > slightly > > > > larger than the first group (i.e., showing a > difference in the > > > > opposite direction). > > > > How would you explain such findings? 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