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.txt3- 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 ?
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:16.9093WM Superior longitudinal fascicle R:2.41935WM Uncinate fascicle R:0.792453Now, 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.txt3- 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?
III- ClusterI 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_alland 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?
Thank you in advance, i highly appreciate it.Walid