Hi,
On 3 Mar 2009, at 06:19, Angelica Hotiu wrote:
> Dear FSL experts,
>
> I was running TBSS analysis using DTI data acquired from 5 control
> subjects
> and 3 subjects with mild traumatic brain injuries. I used FSL4.1.2
> version
> for all preprocessing of the data including TBSS analysis.I am
> interested
> to identify the regions where FA, MD and transversal diffusivity
> indicate
> differences between the two groups. For randomisation procedure I
> used
> first TFCE option .As a result FWE corrected shows the results only
> for MD.
> I couldn't obtain FWE corrected for multiple comparisson for FA and
> transversal diffusivity using TFCE option. Also I was trying another
> option,
> cluster-based thresholding corrected for multiple comparisons using
> different values for threshold .For FA and threshold c = 4, the p
> image,
> tbss_clustere_corrp_tstat2 ,has a p values corrected above 0.928
> which is
> not in the range 0.95-1.Also for a threshold of 0.3 the corrected
> values is
> in range 0.95-1.
> 1)I'm wondering if this threshold value of 0.3 is valid or is to low?
> Is it
> possible a way to calculate the thershold?Is it a paper or manual, to
> clarify, I'm sorry for missing .
It is valid, because randomise will generate valid corrected p-values
regardless of the cluster-forming threshold chosen. However, it is not
normal to set such a low cluster-forming threshold, and you may find
that some reviewers don't appreciate that it is still valid, and
become unhappy! Presumably it results in very large clusters and it
is hard to interpret any useful spatial localisation of effect - in
fact you may simply be testing for whether there is a global shift
between the two groups.
There is no way to "calculate" the threshold - it is an arbitrary user
choice - see discussion on this in the TFCE paper that's just come out
in NeuroImage.
> Also I'm wondering if the output of TFCE
> uncorrected data can be fed into FDR correction.
Yes it can - that is valid.
> 2)If yes, could you please take a look to see if it's correct:
>
> fslmaths tbss_tfce_p_tstat2 -mul -1 -add 1
> tbss_inv_tfce_p_tstat2
> fdr -i tbss_inv_tfce_p_tstat2 -m tbss_tstat2 -q
> 0.05.
Indeed; see
http://www.fmrib.ox.ac.uk/fsl/randomise/fdr.html
>
> 3)I'm not sure what mask image is in -m option.
You should use the same mask that you fed into randomise, i.e.
mean_FA_skeleton_mask
> 4)Could I apply FDR correction to output from cluster based
> thresholding ?
No, randomise doesn't give uncorrected p-values for clusters, just
corrected.
Cheers.
> 5) Is it recommended in this case to randomise using
> cluster-based thresolding corrected for multiple comparison using
> cluster
> mass -C option? What should be the values for C in this case?
> Any suggestions will be greatly appreciated.
> Many thanks in advance.
> Regards,
>
> Angelica
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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