Dear Chao-Gan,
Thank you for your prompt response. We will try some more runs then. I am glad to hear that REST should not differ too much from alphasim. These are great tools.
Best,
Barbara
Barbara L. Ganzel, PhD
Director, Lifespan Affective Neuroscience Lab
Cornell University, Ithaca, NY 14853
lab ph. 607-254-1629
office ph. 254-5395
fx. 607-255-9856
________________________________________
From: YAN Chao-Gan [[log in to unmask]]
Sent: Monday, September 24, 2012 11:51 AM
To: Barbara Ganzel
Cc: [log in to unmask]
Subject: Re: [SPM] Threshold .001 (uncorr)
Dear Barbara,
Since monte-carlo simulation is a random simulation procedure, the cluster size derived this time may differ to next time.
Also, there were slightly difference in SPM's smooth procedure from AFNI's procedure, this will also produce slight difference. (REST is a SPM plugin thus utilize SPM's smooth procedure.)
According to our experience, the cluster size derived from REST should not differ too much from AFNI's alphasim run.
Best,
Chao-Gan
On Mon, Sep 24, 2012 at 11:26 AM, Barbara Ganzel <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Has anyone else had trouble with the matlab monte-carlo simulation that comes with the REST software (www.restfmri.net<http://www.restfmri.net>)? When we compare its results with an AFNI alphasim run, they don't match up (despite using the same initial parameters).
Barbara L. Ganzel
Cornell University, Ithaca, NY
________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]<mailto:[log in to unmask]>] on behalf of James Lee [[log in to unmask]<mailto:[log in to unmask]>]
Sent: Monday, September 24, 2012 11:21 AM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: Re: [SPM] Threshold .001 (uncorr) = fishing expedition?
Gabor,
Yes, uncorrected VOXEL thresholds are often used in publications in
combination with a cluster-size requirement that create CLUSTERS that
are corrected for multiple comparisons.
The argument for the cluster size can come from random field theory
(SPM), or monte carlo simulations as mentioned previously. I often use
the matlab monte-carlo simulation that comes with the REST software
(www.restfmri.net<http://www.restfmri.net>).
My understanding is that when you define a corrected cluster in this
way, you cannot say exactly WHERE in the cluster the activation has
occurred, since no particular voxel is statistically significant on
its own. This point has been made on the list before, although I could
not find it just now.
Jim Lee
On 9/24/12, Roberto Viviani <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Hi Gabor,
>
> maybe I misunderstand your question, but if you already have
> cluster-level significance, then you do not need to consider the
> uncorrected significance in each voxel. Cluster-level significance is
> corrected significance. The uncorrected significance that matters here
> is the one that defined the cluster. All that needs be said about this
> significance is that it should be chosen a priori, not that it should
> be stringent. Hypothetically, you could have chosen this
> cluster-defining uncorrected significance to be p=.20, and the cluster
> significance would still be corrected, if computed appropriately (i.e.
> if you have a good way to compute the null distribution of the cluster
> statistic at this defining threshold).
>
> There are discussions in the literature about using cluster extent and
> cluster peak jointly to improve on the power of the test. These tests
> usually rely on Montecarlo simulations to establish rejection
> thresholds, and are available in packages such as AFNI.
>
> Best wishes,
> Roberto Viviani
> University of Ulm, Germany
>
>
>
> Quoting Gabor Oederland <[log in to unmask]<mailto:[log in to unmask]>>:
>
>> Thanks for the responses so far! The thread Chris has linked to is
>> actually the one I was refering to as well :-) The reason I asked is
>> that there is no real discussion concerning uncorrected
>> voxel-threshold IN COMBINATION with corrected cluster-threshold
>> (corrected as provided by SPM output, so no "corrected" pre-definied
>> value like k > 10).
>>
>> In the salmon poster, the authors "argue that relying on standard
>> statistical thresholds (p < 0.001) and low minimum cluster sizes (k
>> > 8) is an ineffective control for multiple comparisons." In a
>> study of ~ 15 subjects and standard resolution (after normalization)
>> the FWE-corrected cluster-threshold should be something to ~ 50 -
>> 200 voxels, so much higher.
>>
>> The SCAN paper by Bennett and colleagues (2009) does provide any
>> definite answer about corrected cluster-threshold either. They say
>> "It is possible to use the combination of a P-value and a cluster
>> size in a principled way, but it requires computing the proper
>> values for each and every analysis. The cluster size criteria can
>> change quite substantially from dataset to dataset. Further, it can
>> be the case that required cluster sizes become so large that
>> legitimate results with a smaller volume are missed."
>>
>> So, what about this combination of voxel-p = .001 and cluster-p =
>> .05 FWE? Are the limitations (different cluster-threshold in
>> different studies) acceptable or not?
>>
>>
>> Best,
>>
>> Gabor
>>
>
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