Hi - please see the statistics literature on multiple-comparison correction - in general when analysing the whole brain you have to correct for the number of independent tests you carried out - so you have to use the 'corrp' and not the 'p' values, unless you are going to do a separate correction for multiple comparisons, e.g. feeding in the 'p' values into FDR.

TFCE is indeed generally recommended, but voxelwise or cluster-based are also valid outputs from randomise.


On 19 Dec 2009, at 22:03, Ajay Kurani wrote:

Dear FSL Users,

I have been reading documentation regarding Randomise and being that this is
my first analysis I had some questions.  I had a comparison of 17 control
subjects to 17 patients using affine and nonlinear mapping.  After looking
at my tstat1 images for different smoothing (s2 s3 etc) I used randomise to
do 5000 permutations of the data set(after selecting s2).  

randomise -i GM_mod_merg_s2 -m GM_mask -o fslvbm -d design.mat -t design.con
-T -n 5000 -V

The output files are tfce_corrp_tstat and tfce_p_tstat.  When I display
using corrp there are no results while I receive results when using p
(really 1-p)

fslview $FSLDIR/data/standard/MNI152_T1_2mm fslvbm_tfce_corrp_tstat1 -l
Red-Yellow -b 0.949,1
fslview $FSLDIR/data/standard/MNI152_T1_2mm fslvbm_tfce_p_tstat1 -l
Red-Yellow -b 0.949,1

I wanted to find out if it is okay to use the p_tstat1 file to show
significance in results or if we should always only use corrp_tstat?  Is the
difference only that corrp ensures there are less false positives?  Because
the ROI are very small areas I am worried that the corrp_tstat might be
sensitive enough to pick up these areas since they are clearly present in
p_tstat.  Any help or insight would be much appreciated as I am still a bit
fuzzy on the difference between these two parameters.  Also, is TFCE always
recommended or would cluster or voxelwise statistics be recommended if I am
not defining any ROI ahead of time. Thanks.


Ajay Kurani

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)
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