Print

Print
Hi Qasim,

Please see below:


On 28 April 2014 12:29, Qasim Bukhari <[log in to unmask]> wrote:
Dear Experts,
I successfully ran dual regression and randomize on 70 ICs. I have ran a 

Now I m trying to see which of the images survived the 0.95 threshold. I had run a two-group unpaired t-test case using design_ttest2 in my randomise. I m now using the following script to check the results quickly.

for i in dr_stage3_ic0001_tfce_corrp_tstat2.nii.gz; 
do
echo $i `fslstats $i -R`
done


however I m getting two values as result. One is usually 0 and the other varies in every image.
dr_stage3_ic0001_tfce_corrp_tstat2.nii.gz 0.000000 0.849800

1. Can someone explain why 1st value is zero and what does it represent ?? 


The option -R in fslstats shows the range (min and max) of the values in the image.


2. Can someone also please tell the significance of the second value and what does it represent ?


Randomise saves results as 1-p, so your p-value in this example is 1-0.8498 = 0.1502, so there is nothing significant in this image at the level 0.05.

 
3. Since I had two groups, and thus two contrasts, so I have tstat1 and tstat2; however the question that I want to answer is whether there are regions/clusters that have different activations in the two groups.. if only one of tstat, for example tstat1 is greater than 0.95 but tstat2 is less than 0.95; then can I say that this IC cluster was the one differentiating the two groups ?


I think you mean that you'd like to compare the two groups for any difference (either group A>B or A<B), is this right? If yes, create an F-test that includes the two contrasts that test the differences in each direction. To be more clear, look at this example in the manual: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#Two-Group_Difference_.28Two-Sample_Unpaired_T-Test.29, then define an F-test that uses both contrasts.

All the best,

Anderson


 

Thanks a lot for the suggestions
best,
Qasim


Qasim Bukhari

Research Assistant and Doctoral Candidate

Institute for Biomedical Engineering

ETH and University Zurich

Wolfgang-Pauli-Strasse 27, HIT E22

webpages: MR-page

http://www.biomed.ee.ethz.ch/people/sybukhar