29 May
2018
29 May
'18
1:29 p.m.
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 <dgreve@mgh.harvard.edu mailto:dgreve@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, pedrogomesrosa@gmail.com <mailto:pedrogomesrosa@gmail.com> wrote: >> >> Dear Doug >> >> -- >> Pedro >> >>> On May 15, 2018, at 13:36, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto: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/MultipleComparisonsV6.0Perm <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 >>>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto: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>> >>>> <mailto: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-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>> >>>>> <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>>> >>>>> <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 <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. >>>>> > > >>>>> > > >>>>> > > _______________________________________________ >>>>> > > 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>>> >>>>> > <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 <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>>> >>>>> > >>>> <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>>> >>>>> <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 <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>>> >>>>> > >>>>> >>>> <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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