So the maximum is positive, but the mean is negative? When you look at the uncorrected p-values, can you actually find this? My guess is that the cluster must be largely negative, so I would report that
On 05/23/2018 03:52 PM, Pedro Rosa wrote:
External Email - Use CautionDear Doug, Many thanks. I ran the analysis with 'abs', 'pos' and 'neg' testing. All clusters (including the 'problematic' cluster on the medialorbitofrontal region) are present in 'abs' and 'neg' testing summaries, and not present in 'pos' testing summary. This medialorbitofrontal cluster shows a direction of effect when I consider the contrast (and the maximum statistical value signal) and the opposite direction when I analyze groups means. How should I proceed to report such result? Best, Pedro. PS: I apologize if I sent a number of empty emails to the list in the last hours.
On May 23, 2018, at 13:30, pedrogomesrosa@gmail.com wrote:
Dear Doug
-- Pedro
On May 15, 2018, at 13:36, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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/MultipleComparisonsV6.0...
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 <dgreve@mgh.harvard.edu mailto:dgreve@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 <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu
<mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>> wrote:sorry, one more thing. Can you send your mri_glmfit-simcommand 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 thecluster> 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 1and 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 > <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>><mailto: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 thatintriguedme: 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 meansfrom that> cluster > > (as available in the glmdir), the second group hadvaluesslightly > > larger than the first group (i.e., showing adifference in the> > opposite direction). > > How would you explain such findings? Must I havecommitted a> mistake > > in the analysis or its interpretation? > > Best, > > Pedro Rosa - University of São Paulo - Brazil. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>><https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>><https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline<http://www.partners.org/complianceline><http://www.partners.org/complianceline<http://www.partners.org/complianceline>>> <http://www.partners.org/complianceline<http://www.partners.org/complianceline><http://www.partners.org/complianceline<http://www.partners.org/complianceline>>> . If the e-mail was sent> to you in error > but does not contain patient information, pleasecontact the> sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>_______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer