Alex,
In qdec, currently it's limited to two discrete factors, although using
mri_glmfit (upon which qdec is built) you could formulate your own
contrast matrices having >2 discrete factors.
Nick
On Wed, 2007-12-26 at 13:32 +1100, Alex Fornito wrote:
> Great. Thanks for the feedback.
>
>
> On
On Fri, 21 Dec 2007, Alex Fornito wrote:
Hi,
After wrestling with this a bit, I think I get the idea (finally!). Just to
confirm:
1- set a primary threshold in the mri_glmfit command, e.g., --sim perm 5000
1.3 will run 5000 permutations with the primary cluster forming threshold set
at .05.
Thanks Pratap and Cameron.
When I said primary cluster forming threshold, I did mean the vertex-wise
p-value. I imagine it should be reported, as it will affect the clusters
you subsequently extract (lower p-values would lead to larger clusters
needed for significance (??)).
Does anyone have any
Hi,
Just th9ought I would chime in here. I have the same understanding as
Pratap as long as by "primary cluster forming threshold" you are referring
to is the vertex wise p-value. The cluster wise p-value you choose after
the simulation does not have to be derived from this value. But perhaps
both
Doug,
please correct me if i am wrong and add if need to.
> Hi,
> After wrestling with this a bit, I think I get the idea (finally!).
> Just to confirm:
>
> 1- set a primary threshold in the mri_glmfit command, e.g., --sim
> perm 5000 1.3 will run 5000 permutations with the primary cluster
> formi
FDR assumes that the collection of values has both positives and
negatives. It assumes that the pvalues of the negatives are uniformly
distributed between 0 and 1, and this model is used to estimate the
total number of positives (both true and false). When you cluster, you
are setting all voxel
yeah, I've replaced the input with the sig.mgh for the contrast of
interest, which retruns something more plausible. Thanks again, and sorry
for the confusion.
Ta,
Alex
> I noticed that you are using contrasts.sig.mgh as the input to
> mri_surfcluster and that the source frame is 0. contrasts.si
Sorry, can I ask why the clustering step would invalidate FDR?
>From my understanding, FDR allows you set a limit on the number of false
positive in a family of contrasts reaching significance at a nominal
threshold. I would like to this nominal threshold using cluster stats
(e.g., p<.05, cluster
Thanks for your help Pratap.
I've actually been trying to follow the tutorial and was running
simulations initially, but when I tried to re-trace my steps I ended
omitted them because I forgot they were necessary for mri_surfcluster.
Either way, the results are the same- I still get one who
Hi all,
I was hoping someone could help me with the problem below. I'm a little
stuck on my analysis.
Thanks,
Alex
> On 11/28/2007 07:43 PM, Alex Fornito wrote:
>> Hi,
>> I have run qdec for a simple contrast comparing thickness across the
>> cortical surface between a patient and control group.
Hi,
I have run qdec for a simple contrast comparing thickness across the
cortical surface between a patient and control group. Not much
survives vertex-wise FDR correction, and I would like to try cluster-
based thresholding. I would like to make sure I understand the inputs
to the command.
Not quite yet, still tweeking on it
Sasha Wolosin wrote:
Dear all,
Has the January dev release incorporated the new corrections for
multiple comparisons in group analysis, e.g. cluster thresholding?
Thanks,
Sasha
Sasha Wolosin
Research Assistant
Developmental Cognitive Neurology
Kennedy Krieg
Dear all,
Has the January dev release incorporated the new corrections for
multiple comparisons in group analysis, e.g. cluster thresholding?
Thanks,
Sasha
Sasha Wolosin
Research Assistant
Developmental Cognitive Neurology
Kennedy Krieger Institute
707 N. Broadway
Baltimore, MD 21205
ph: (443) 9
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