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
> <dgreve@mgh.harvard.edu <mailto:dgreve@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>).
>     > Best,
>     > Pedro Rosa.
>     >
>     > On Mon, May 14, 2018 at 5:42 PM, Douglas N. Greve
>     > <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>
>     <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@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? Must I have committed a
>     >     mistake
>     >     > in the analysis or its interpretation?
>     >     > Best,
>     >     > Pedro Rosa - University of São Paulo - Brazil.
>     >     >
>     >     >
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