Hi,
On 21 Dec 2007, at 22:06, Naama Barnea-Goraly wrote:
>
> Dear FSL list,
>
> Questions about extracting values from clusters of significant FA
> differences generated in TBSS:
>
> 1. How can I get a list of clusters by size with coordinates of peak
> differences ect (kind of like the table in SPM?). I tried to use
> cluster on my tbss_maxc_tstat image but I get only one cluster and
> it looks like there should be more. Plus I don't get the values of
> peak differences within the cluster.
If you mask the tstat image with the maxc, something like
fslmaths grot_maxc_tstat1 -thr 0.95 -bin -mul grot_tstat1
clusters_grot_tstat1
then you can feed this output into cluster and tell it to output local
maxima etc. This should give you everything you want; it just won't
ive you p-values for the clusters, but you already know that all
clusters are p<0.05 corrected.
> 2. How to separate the clusters to extract values from each cluster
> separately?
The above should do that, in the same way that FEAT does. Also, if you
use the -o option to cluster, you can get an image of cluster-index-
number output as well.
> Once I have the peak coordinates with the cluster I can generate the
> list of values using fslmeants - but what radius does it use? If I
> want to get values of the voxel only within the limits of my
> significant cluster do I use:
>
> fslmeants -i all_FA_skeletonised -c x, y, z -m my_mask ?
Yes - you can select individual clusters by running the cluster-index-
number output image through fslmaths first.
Cheers.
>
>
> Is there a manual for these operations? If so I am sorry for missing
> it..
>
> Thank you so much for your help,
>
> Naama
>
>
> Naama Barnea-Goraly M.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University Division of Child and Adolescent Psychiatry
> 401 Quarry Rd. MC 5795
> Stanford University School of Medicine
> Stanford, CA 94305-5795
> fax: (650) 724-4794
> Phone: (650) 724-3779
>
>
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