PALM(permutation test)

Submitted by kato7kato7 on

Dear experts

I did a correlation analysis with PALM. Setting of PALM is 5000 permutations, cluster forming threshold 2.3, TFSE, gamma approximation. And I got results which are uploaded. 

To explore the results, I used DPABI Viewers. To interpret the results, How should I set the parameter including P -value in "overlay configure?" And what's the exact difference among R_clustere_rstat, R_tfce_rstat and R_vox_rstat? does the setting of parameter in overlay configure vary according to R_clustere_rstat or R_tfce_rstat or R_vox_rstat? 

If I apply p value 0.05 or 0.01 due to FWEP or FDR, how large the threshold of cluster size could I set? In case of TFCE, it doesn't need a threshold for cluster size. If then, when I interpret the results of tfce image by cluster report, how many voxels of cluster are meaningful for determining whether that cluster is significant? 

And at the viewer results, when I upload r_tfce_rstat_fwep image, brain is shown as yellow. Is it because I omitted global signal regression? And when I want to subtract these yellow signal from the image for making figure, how could I process it? 

 

Best, Dong Woo 

 

 

kato7kato7

Tue, 01/03/2017 - 05:52

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Could anybody show me the direction of dealing with permutation test? 

The number of my sample is small, therfore the efficacy of permutation test may be restrictive. 

Despite, I just wish to interpret the results of permutation test in regardless of the efficacy of permutation test. 

Best, Dong woo 

 

 

 

 

YAN Chao-Gan

Tue, 01/03/2017 - 11:53

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You can have a look at this PPT: http://lab.rfmri.org/Course/V2.1CH/4_Course_R-fMRI_Data_Processing_StatisticalAnalysis.pptx Slide 55

If you understand Chinese, then you can look at http://rfmri.org/Course#Chinese Part IV Video. Or wait for the release of the English version.

1._vox_tstat.nii is the T value of a voxel.
2. _vox_tstat_uncp.nii is the p value corresponds to the rank of the observed T value within the permutations FOR A GIVEN VOXEL (the null distribution is the permuted T values of that given voxel). Computing the rank is one of the ways in which the p-value can be obtained (it's then divided by the number of permutations).
3._vox_tstat_fwep.nii is the p value corresponds to the rank of the observed T value within the permutations of maximum T values across all the voxels (the null distribution is composed by the maximum T value across all the voxels for each permutation). For the corrected, the distribution of the maximum is used as reference, and the rank (or quantile) of a given voxel in relation to that distribution is used to obtain p-values.
3._clustere_tstat.nii is simply the size (in voxels) of the cluster. This number acts as the test statistic.
4. _clustere_tstat_fwep.nii: p-values computed in the same way as 3, i.e., using the distribution of the maximum cluster size.
5.The TFCE maps are similar to Points 1, 2 and 3.
 
Best,
Chao-Gan

TFCE - is there an English version of this tutorial below?-

http://lab.rfmri.org/Course/V2.1CH/4_Course_R-fMRI_Data_Processing_StatisticalAnalysis.pptx Slide 55 

I have a fairly decent sample size (Group 1 ~60+ patients, Group 2 ~45 controls); I see significant differences with GRF at voxel p < .001 and cluster p < .05. But for TFCE, there is no significant difference. 

1) After I run the PALM, for viewing the results, I pick the file "tfce_tstat.nii" and then use the "tfce_stat_fwep.nii" file as the mask, is this correct?

Thank you.

 

You can have a look here: http://rfmri.org/content/permutation-test-dpabi

We will produce an english version of vedio later this year.

It's possible that you don't have results in permutation test with TFCE but have with GRF.

Thank you for the link. This is what I was looking for, thanks!

"To visualize the result of permutation test, open the “_vox_tstat.nii” as an overlay in DPABI_VIEW, click the “Apply a Mask for Additional Threshold” button in “Cluster” menu, select proper result file (e.g. “T2_tfce_tstat_fwep.nii”) and modify the threshold. A statistical map after permutation test will be shown in DAPBI_VIEW."

 

Best.

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