Dear Gwenaelle,
I am very sorry to bother you again. I tried FDR and TFCE. I would like to clarify few things, first i will tell you what i did,
I followed the guidelines from FDR website
1) fslmaths fslvbm_s4_tfce_p_tstat2 -mul -1 -add 1 1_minus_fslvbm_s4_tfce_p_tstat2 (where fslvbm_s4_tfce_p_tstat2 is my uncorr p value image for N-C comparison using TFCE)
2) fdr -i 1_minus_fslvbm_s4_tfce_p_tstat2 -o result -m GM_mask -q 0.05 (Is it correct to specify GM_mask here)
the result from this step is "Probability Threshold is: 0" .Is this threshold correct?
3) Since my threshold value is 0 the next step (i used 1- thr which is 1)
fslmaths fslvbm_s4_tfce_p_tstat2 -thr 1 thresh_fslvbm_s4_tfce_p_tstat2
so an image full 0 is the end result.
Your comments on this.
Thanks
Regards
venkateswaran
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
Sent: Thu 10/8/2009 1:12 PM
To: [log in to unmask]
Subject: Re: [FSL] Re : [FSL] Contrast matrix for one way ANOVA-VBM
Hi,
> You are right that my sample size for control is less than
> the sample size for D and other groups.
I was more talking about the n of B, C and E compared with D.
> I looked at the uncorrected p values i could see some
> significant differences between control and other patient
> groups,
If they are uncorrected, they are *not* significant. But they might indicate that it would be if you use a more sensitive way of correcting for multiple comparisons...
> i also looked unthresholded corrected p-values
> (_tstat file extension am i correct)
Hmmm, no. Please have a look at the randomise manual (www.fmrib.ox.ac.uk/fsl/randomise). Corrected p-vals are *_corrp_*, uncorrected p-vals are *_p_*.
> I would like
> to try FDR and TFCE correction can you please tell me how
> can i run these stats on this data.
Again, please have a look at the end of the FSL-VBM manual, the randomise manual and the fdr manual (www.fmrib.ox.ac.uk/fsl/randomise).
Cheers,
Gwenaelle
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