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Hi Freesurfers users,

I am looking on cortical thickness after ischemic stroke, especially stroke with cortical involvment. Freesurfer is validated in this population, Li, Q. (2015). Cortical thickness estimation in longitudinal stroke studies: A comparison of 3 measurement methods. NeuroImage : Clinical, 8, 526–535.

When I check the surfaces on Freeview, cortical infarcts are excluded (which is great because of the major anatomy distorsion) but the pial and white surfaces (in contact to the area excluded) are different from zero. It seems that Free-surfer still calculates the cortical thickness as an average measure of the surfaces in contact to the area excluded (which doesn't have any grey matter !). I can send you a picture to illustrate my question.

I am wondering: how does Freesurfer calculate the surfaces in contact to a cortical area excluded ? 

Thanks a lot

Guillaume
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pedro Rosa <pedrogomesrosa@gmail.com>
Sent: Sunday, May 27, 2018 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Contrast interpretation - between-groups mean
 

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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?

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.
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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