Hi Walid,

Please see below:

On 24 January 2017 at 00:27, Walid Yassin <[log in to unmask]> wrote:
Dear FSLers,

>>>Sorry for double posting, but i didn't include a title for my post yesterday for archiving. 
Also it wasn't forwarded. Please check below.<<<


I would like to ask you  for a confirmation and some help please!


I- I did all TBSS steps between 2 groups and got the results:

tbss_tstat1.nii.gz, tbss_tstat2.nii.gz, tbss_tfce_corrp_tstat1.nii.gz, tbss_tfce_corrp_tstat2.nii.gz, etc..

I want to check if there is a relationship between the significant areas that resulted and my clinical data so i did:

1- fslmaths tbss_tfce_corrp_tstat1.nii.gz -thr 0.95 -bin sig_results_mask
2- fslmeants -i all_FA_skeletonised -m sig_results_mask -o sig_FA.txt
3- Got the results and correlated with clinical data.

Is this OK? Should i have used tbss_tstat1.nii.gz instead of tbss_tfce_corrp_tstat1.nii.gz ?



This isn't ok I'm afraid. This is what has been known as "voodoo" correlations: it's a circular analysis that shouldn't be used.

 
II- I wanted to check which areas are my significant voxels in. So i did: 
 
1- atlasquery -a "Juelich Histological Atlas" -m significant_results_mask.nii.gz

Let’s say these are my only results:

WM Optic radiation R:16.9093
WM Superior longitudinal fascicle R:2.41935
WM Uncinate fascicle R:0.792453

Now, if i want to do the same analysis as before, meaning if i want to check significant voxels in the "WM Optic radiation R” ROI only, and correlate those to my clinical data. should i do:

Get the "WM Optic radiation R” ROI from the atlas. Let’s say i call it optic_rr.nii.gz So it will be: 

1- fslmaths tbss_tfce_corrp_tstat1.nii.gz -thr 0.95 -bin sig_results_mask
2- fslmeants -i optic_rr -m sig_results_mask -o sig_FA_oprr.txt
3- Got the results and correlated with clinical data.

-Is this correct? 
-Also, which atlas is better to use? Should i try several white matter atlases and see which ones my voxels hit most? 


For the reason above, don't do this analysis.

However, if you were do to it, you could use the region from the atlas directly as the mask with the command fslmeants.



III- Cluster

I am wondering after i have done the above whether there is merit in doing cluster analysis!

I already did the following to report cluster size:

cluster -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95 --mm > cluster_95_all

and Got 8 clusters ranging from voxel# 1 to 750.

Is doing further cluster analysis meaningful? such as z- or t- stats per cluster?

Last question. Can clusters have labels about the regions the contain them?
For example cluster 8 is contains 750 voxels, can i know which regions in a JHU atlas are in this cluster?


This is fine. It will list the coordinates of the significant regions. For the region names, you can overlay on a structural image and compare with the actual brain anatomy, or use a tool such as the command autoaq (shipped with FSL).

All the best,

Anderson

 




Thank you in advance, i highly appreciate it.

Walid