Correction: the two lines need to be:
global defaults
defaults.stats.topoFDR = 0;
On Fri, Mar 23, 2018 at 11:08 AM, Thomas Nichols <
[log in to unmask]> wrote:
> Dear Patrick,
>
> Can someone explain how exactly do we use topological FDR in SPM12? I have
>> tried to follow some old posts but I am a little confused.
>>
>> I gather that we first start by looking at the uncorrected results at a
>> small T value (say 3) or else by setting p<0.001. After this we look at the
>> FDRc value at the bottom of the results table. This is the extent threshold
>> value above which all qFDR-corr values (cluster-level) will be less than
>> 0.05. Then we simply re-run the results, select uncorrected, set p<0.001
>> and set the extent threshold to that FDRc value?
>>
>
> Topological FDR refers to two different types of inference, clusterwise
> FDR and peak-wise FDR. You should commit to one or the other before you
> see the data.
>
> For either clusterwise FDR and peak-wise FDR, you're right, you need to
> set an uncorrected threshold, p<0.001 is reasonable.
>
> You can peruse the results table seeing which clusters are significant or
> not according to q_FDR-corr under cluster-level or peak-level. If you'd
> like to filter the results and only show significant peaks/clusters, then
> you can re-do results or just go to the interactive window menu, Contrasts
> -> Significance Level -> Change...
>
> Let's say I'm doing FDR-corrected cluster inference; say I see FDRc of 38
> in the footer. I do "Change ..." and now I set "p-value adjustment" to
> "none", "threshold {T or p value}" to the cluster-forming threshold I used
> before, e.g. 0.001, and then I enter the extent threshold FDRc, i.e. 38.
>
> If I'm doing FDR-corrected peak inference; I see FDRp of 8.598 in the
> footer. I do "Change ..." and now I set"p-value adjustment" to "none",
> "threshold {T or p value}" to the FDRp of 8.598, and extent I leave at
> the default of 0.
>
> In the former, you'll see the same FDR-corrected cluster p-values; in the
> latter, for FDR-peak inference, I'm afraid the FDR-corrected peak p-values
> change because they are dependent on the screening threshold... i.e. the
> critical FDR-corrected peak threshold of 8.598 was dependent on use of a
> screening threshold of P<0.001, and now that you've changed it, all of your
> topological FDR p-values will change.
>
>
> You may find it more rewarding to simply disable topological FDR; for one
> session, you can use these two lines
>
> global defaults
> defaults.stats.topoFDR = 1;
>
>
> or, permanently, editing spm_defaults.m so that line 79 reads:
>
> defaults.stats.topoFDR = 0;
>
>
> You will then only have FDR-corrected voxel-wise p-values provided, but
> the will not be dependent on the screening threshold.
>
> -Tom
>
> __________________________________________________________
> Thomas Nichols, PhD
> Professor of Neuroimaging Statistics
> Nuffield Department of Population Health | University of Oxford
> Big Data Institute | Li Ka Shing Centre for Health Information and
> Discovery
> Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom
> T: +44 1865 743590 <01865%20743590> | E: [log in to unmask]
> W: http://nisox.org | http://www.bdi.ox.ac.uk
>
--
__________________________________________________________
Thomas Nichols, PhD
Professor of Neuroimaging Statistics
Nuffield Department of Population Health | University of Oxford
Big Data Institute | Li Ka Shing Centre for Health Information and Discovery
Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom
T: +44 1865 743590 | E: [log in to unmask]
W: http://nisox.org | http://www.bdi.ox.ac.uk
