Dear FSL experts,
I am doing some preliminary analysis on 42 controls subjects that we have.
After running randomise on FA skeleton by using the command:
randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t
design.con -n 1000 --T2 -V -x
I didn't get any significant results by looking at "tbss_tfce_corrp_tstat2.nii.gz" file (the
corrected p stats file), which is expected, since the purpose of my analysis is basically
exploring.
So I look at the "tbss_tfce_p_tstat2.nii.gz" file (showing uncorrected p) in order to get a
sense of what regions might show up. By set the threshold to (1-p)>0.99, and I did see
two region that really support my hypothesis. But I do not know how to generate a
report that show the cluster size of those regions.
What I really would need is a command that might be similar to easythresh, which I can
specify the threshold for "tbss_tfce_p_tstat2.nii.gz" and cluster size in a sensible way.
I did try easythresh on the raw t-stats data, but it seems like there is a discrepancy
between the generated outputs and what I see on the thresholded
"tbss_tfce_p_tstat2.nii.gz". I am not sure which one makes more sense to look at. The
command I tried with easythresh is:
easythresh tbss_tstat2.nii.gz mean_FA.nii.gz 3.307 0.001 mean_FA_mask.nii.gz
Easythresh_3.307_0.001_tstat2
Thank you for any input.
Best wishes,
Yi-Shin
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