Hi Roger,
> 1. Is there any way to use the cluster program (or
> any other program in
> FSL) to capture both MNI coordinates and corresponding mean
> FA values (for
> patient and control groups) of ALL voxels that are
> significantly different
> between the compared groups?
You can use fslmeants on your mean FA map, using a mask that you can create by thresholding/binarising your significant results, e.g.:
fslmaths -i tfce_corrp_tstat1 -thr 0.95 -bin mymask
fslmeants -i mean_FA -m mymask -o all_voxels_significant.txt --showall
> 2.Can a report be generated listing the
> total count of significantly
> different voxels for each involved white matter structure,
> as identified by
> the voxels’ MNI coordinates and corresponding labels in
> the JHU White-Matter
> Tractography Atlas?
I would then intersect each ROI of the atlas (see previous posts on this) with your mask of significant results, e.g.:
fslmaths mymask -mas uncinate mymask_unc
To get the number of voxels, just do a fslstats -V on each of your new masks.
> 3. Can mean FA also be calculated (for patient and
> control groups) for
> these significantly different voxels grouped by white
> matter structure?
Just repeat the fslmeants command above with the appropriate new masks.
Hope this helps,
Gwenaelle
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