External Email - Use Caution Hi, Doug. I manually checked for the sig values, and all I got were positive. Is this unexpected?
Should I write someone to get those binaries? I tried to run it again, and was not successful. Many many thanks! -- Pedro > On May 29, 2018, at 12:29, Douglas Greve <dgr...@mgh.harvard.edu> wrote: > > > >> On 5/27/18 3:33 PM, Pedro Rosa wrote: >> >> >> Hi, Doug. >> For this specific 'problematic' cluster, the maximum statistical value from >> the cluster summary is negative, that indicates a direction of result >> (considering the contrast matrix I used) opposite to the one I >> get when I compare means. >> I inspected p-values from sig.mgh (and also p-values masked for surviving >> clusters) and all seem positive. I could not actually get how inspection >> sig.mgh may help to solve this issue. Can you clarify this point, please? > I mean do you find both positive and negative values in the sig.mgh in the > vertices of the problematic cluster? I suppose it is possible, I've just > never seen it before. >> >> Following your comment on the 1.3 threshold, I read the paper and the >> permutation page from FreeSurfer wiki, and tried to run mri_glmfit-sim with >> perm function (after mri_glmfit with -eres function) using FS6 twice, and it >> seems to take many hours (~ 26 hours) to run (I am using a regular Mac >> computer, not a cluster), while the wiki mentions it should take 20 minutes. >> I got this message while running it: 'INFO: design matrix is not orthogonal, >> but perm forced'. Also, it ended with this error: ERROR: Option --vwsigmax >> unknown., and it dit not creat the perm* files. I attached the log, in case >> you want to inspect it. > If you are on a mac, we will have to get new binaries for you. Rob, can you > get a mac version of mri_surfcluster to Pedro? > > Also, don't run mri_glmfit-sim with --bg 1 as it causes really long run times > for reasons I don't understand. If you are running with multiple processors, > then use --bg N where N is the number, but if N=1, just leave off --bg > entirely. > >> Also, I changed the mri_glmfit-sim file regarding the .csh file path >> ($FREESURFER_HOME/sources.csh to /SetUpFreeSurfer.csh) before running it (it >> could not find sources.csh). >> Many thanks, >> Pedro. >> >> >> >> >>> On Wed, May 23, 2018 at 6:45 PM, Douglas N. Greve <dgr...@mgh.harvard.edu> >>> wrote: >>> 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 Caution >>> > >>> > Dear 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, pedrogomesr...@gmail.com wrote: >>> >> >>> >> Dear Doug >>> >> >>> >> -- >>> >> Pedro >>> >> >>> >>> On May 15, 2018, at 13:36, Douglas N. Greve <dgr...@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/MultipleComparisonsV6.0Perm >>> >>> >>> >>> >>> >>>> 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? Must I have >>> >>>> committed 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. 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