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> 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 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/MultipleComparisonsV6.0Perm
>>>
>>>
>>>> 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>> 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-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
>>>>>       > <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.
>>>>>       >     >
>>>>>       >     >
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