The max is the -log10(p), bounded below by -log10(CWP) for positive
correlations Hence with an -log10(CWP) of 4, the Max
will be greater than 4, and will specify the maximum -log10(p) value in that
cluster, occuring at VtxMax
Is this right for -log10(p) kind if input? This is how i have been
interpreting my results so far, and i just want
to be sure......
I was also wondering why -log10(p) transformation has been used for this
kind of visualization? SPM displays
SPM_{z} scores, and that seems a better way to report the spms. Is -log10(p)
an approximation to z-scores ?
sid.
On Thu, Jun 4, 2009 at 9:53 AM, Judith Segall <jseg...@mrn.org> wrote:
> Thanks, for you responses Doug and Pratap. But, both of your responses need
> more clarification, because I believe that we are not all referring to the
> same 'max'.
>
> Doug:
>
> I understand that when I display the sig.cluster.mgh that the a CWP value
> of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it
> is the -log10(p). However, in this case, which is about the cluster growing
> summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and
> the CWP is 0.08250. Or an additional example form another
> sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192.
> ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP
> CWPLow CWPHi NVtxs Annot
> 1 -4.310 40526 376.78 -12.0 -66.1 5.4
> 0.01920 0.01750 0.02100 706 lingual
>
> In Pratap's email his answer to my question of what is the max in the CWP
> is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that
> cluster." Which, is stating that it is both the thickness and the pvalue. I
> really think that it is thickness measure, but need some clarification from
> mgh.
>
> So, is the Max in column 2 of the cluster growing summary report, from
> monte carlo simulations, thickness?
>
> Thanks,
>
> Judith S.
>
> On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu
> > wrote:
>
>> It will be whatever you used as input. In this case, it is the -log10(p)
>> value of the maximum in the cluster (not the thickness value).
>>
>> doug
>>
>>
>> Pratap Kunwar wrote:
>>
>>> Hi Judith,
>>>
>>> Yes thickness. The MAX indicates the maximum -log10(pvalue) in that
>>> cluster.
>>>
>>>
>>>
>>>> Hi all. After looking over our monte-carlo results, I a simple question
>>>> about the sig.cluster.summary output.
>>>>
>>>> Is the " Max" in column 2 below a measurement of thickness?
>>>> thickness, is the correct interpretation the following: the most
>>>> significant
>>>> cluster is in the laterorbitofrontal region.
>>>>
>>>>
>>> yes at lateral orbital frontal.
>>> The max vertex in that
>>>
>>>
>>>> cluster
>>>> has an average thickness of 3.312 mm and the negative directionality
>>>> indicates that it is thinner in that region than in the fsaverage (from
>>>> freesufer) used in the group analysis/simulations?
>>>>
>>>>
>>> yes you are correct.
>>>
>>>
>>>> If it does not refer to thickness, is it a statistic, etc?
>>>>
>>>> # Minimum Threshold 2
>>>> # Maximum Threshold infinity
>>>> # Threshold Sign abs
>>>> # AdjustThreshWhenOneTail 1
>>>> # Area Threshold 0 mm^2
>>>> # CSD thresh 2.000000
>>>> # CSD nreps 10000
>>>> # CSD simtype mc-z
>>>> # CSD contrast lh-Avg-thickness-CAQ-CCI
>>>> # CSD confint 90.000000
>>>> # Overall max 2.05497 at vertex 92846
>>>> # Overall min -3.3122 at vertex 60632
>>>> # NClusters 11
>>>> # Total Cortical Surface Area 65416.6 (mm^2)
>>>> # FixMNI = 1
>>>> #
>>>> # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP
>>>> CWPLow CWPHi NVtxs Annot
>>>> 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250
>>>> 0.07900 0.08600 341 lateralorbitofrontal
>>>> 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620
>>>> 0.52980 0.54260 212 rostralmiddlefrontal
>>>> 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360
>>>> 0.35740 0.36980 337 superiorfrontal
>>>> 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240
>>>> 0.62620 0.63860 79 bankssts
>>>> 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240
>>>> 0.62620 0.63860 38 superiorparietal
>>>>
>>>> I am trying to finish writing up my results and just need answer to this
>>>> question to continue.
>>>>
>>>> Thanks,
>>>>
>>>> Judith S.
>>>> Mind Research Network
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>>>>
>>>
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>>>
>>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> In order to help us help you, please follow the steps in:
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
>>
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