Hi everyone,
I posted a message on the list yesterday:
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?
A2=ind0903&L=SPM&P=R53442&X=32BF90638ADA3D24CE&Y=w.mcgeown%
40hull.ac.uk
I have also pasted this message below for your convenience.
I would like to thank Jonathan Peelle for his helpful comments in response to
my message:
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?
A2=ind0903&L=SPM&P=R54747&X=32BF90638ADA3D24CE&Y=w.mcgeown%
40hull.ac.uk
Also pasted at the bottom of this message.
However I am still curious about the later parts of my original message
regarding SVC when using VBM and in fMRI. Maybe someone could comment
on these sections as well please?
It would be much appreciated if there was someone could find the time to do
this.
Thanks
Will
Hi all,
Hopefully someone can help me with these somewhat basic questions.
I have trailed the archives and still remain somewhat confused. I think by
laying these questions out in a straightforward and comprehensive manner,
maybe I can get a straightforward and understandable response.
The first set of questions involve VBM.
When carrying out voxel based morphometry in SPM5 after pressing for results
out of the options FWE, FDR and none, I select none. The results I have do
not survive this correction for multiple comparisons.
I then choose e.g. p<0.01 and an extent threshold of zero.
In the results table that I get, I can report the z-values (or T-values) which
correspond to certain coordinates, but if I wanted to report p-values as well
which column should I report in my manuscript? As far as I know there is an
issue with using cluster p-values when using VBM. Should I therefore report
the voxel P FWE-corr, the voxel P FDR-corr, or the P uncorrected voxel value?
Also, if some are significant at the voxel P FWE-corr level and others are only
significant at voxel P uncorrected level what should I do here? E.g. report P
FWE-corr only and disregard the others? Or report a combination of p-values
(showing the distinction between thesein the paper in some way)?
Please can whoever answers these questions be very clear in their response
as I would like to be very accurate with the reporting of my results.
Also I have an a priori assumption that there will be correlations in a certain
areas. When this is the case I think it is appropriate for me to select the
cluster maxima in my a priori region and click SVC e.g. at 10mm. I will report
which clusters have received a SVC in the paper. After doing this the p-
values of course change and again I wonder which column I should report e.g.
should it now be the cluster uncorrected p-value (or do I leave this alone
completely with VBM?), the voxel P FWE-corr or the voxel P FDR-corr?
The last question regards fMRI.
Here it is valid to use the cluster P corrected values. I can report these in my
paper and that is fine.
When I carry out a SVC e.g. 15mm, on the maxima of a cluster (in an a priori
area) in this case which P-value should I report? Should I report the cluster P
uncorrected value (as the expected number of voxels per cluster will be
reduced)?
I take it that I should not report the cluster P corrected value as the expected
number of clusters might well be reduced below one with such a small area and
these P-values would therefore be misleading?
Can someone please clarify and answer all these questions please. I am not a
mathematician or statistician, so please keep the answers basic and
understandable. Saying that I want to make sure I report all of these things
correctly.
Thanks in advance.
Will
Hi Will
I don't know if I can address everything you ask, but I'll see if I
can help a bit. The short answer is probably that there is no single
correct way to do things; the important thing is to provide enough
information so readers know exactly what threshold you used.
> The first set of questions involve VBM.
> When carrying out voxel based morphometry in SPM5 after pressing for
results
> out of the options FWE, FDR and none, I select none. The results I have do
> not survive this correction for multiple comparisons.
> I then choose e.g. p<0.01 and an extent threshold of zero.
> In the results table that I get, I can report the z-values (or T-values) which
> correspond to certain coordinates, but if I wanted to report p-values as well
> which column should I report in my manuscript? As far as I know there is an
> issue with using cluster p-values when using VBM. Should I therefore report
> the voxel P FWE-corr, the voxel P FDR-corr, or the P uncorrected voxel
value?
First, you are correct that the random field theory (RFT)-based
cluster level p values should generally not be used for VBM because
the data aren't uniformly smooth (i.e. there is a nonstationarity
problem). There is, however, a nonstationarity toolbox that can
correct for this, allowing you to use cluster-level correction:
http://fmri.wfubmc.edu/cms/NS-General
Regarding what to report, generally you will want to report the
voxel-level statistic that was used for all of your reported voxels,
and then in addition, some additional information about a
cluster-level p value (if you use one). In your case as you describe,
you would just describe the results as using a voxelwise threshold of
p < .01, with no correction for multiple comparisons. If you use a
cluster-level threshold, include that as well. In other words, the
same standard information you would find in most fMRI papers.
If you had done an analysis using FWE or FDR to correct for multiple
comparisons, this would apply to all voxels in your results, and you
would report it accordingly.
In the case in which an uncorrected value is used (like you have), the
FWE or FDR values for the peaks are sometimes (but I think not often)
used as a sort of additional criteria. For example, sometimes people
will use a voxelwise threshold of p < .01, but only report clusters in
which the peak voxel is FWE < .05. (I always find this a little bit
odd as typically conclusions are drawn about the whole extent of the
cluster, but only the peak voxel passes a more stringent threshold.)
Generally I think it is more straightforward to have a voxelwise p
value, and optionally, a cluster-level p value, and leave it at that.
> Also, if some are significant at the voxel P FWE-corr level and others are only
> significant at voxel P uncorrected level what should I do here? E.g. report P
> FWE-corr only and disregard the others? Or report a combination of p-values
> (showing the distinction between thesein the paper in some way)?
Generally you would want to pick a single criterion and stick with
that for the whole analysis. For example, if you decide p < .01
(uncorrected) is appropriate, you would just use this, and not bother
noting which voxels surpass this. However, if you are (probably
correctly) worried that reviewers will think this threshold is too
lenient, you might want to use a voxelwise threshold of FWE < .05, in
which case you would disregard voxels that don't reach this level.
I will leave the SVC questions to someone with more experience in
those matters. Good luck! Hope this helps.
Jonathan
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