Hi,
Note that 0.995 corresponds to P<0.005, corrected, i.e. more
conservative than most people use.
You can use the "Cluster" program and the --osize option to get an
image of cluster sizes output, which you can then threshold in
fslmaths. This program can also give you the table listing the
clusters.
Cheers.
On 24 Nov 2008, at 05:07, liang wang wrote:
> Dear FSLers,
>
> Using TBSS analysis pipeline, I got some stat images. Firstly I used
> p > 0.995 to threshold these stat images. Thus, some very clusters
> (e.g. 1 voxel) were also survived. Then we want to use cluster size
> (e.g. 10 voxels) to threshold the resulting images. Two questions
> need your help!
>
> 1) how to use cluster threshold to do this work in FSL software,
> similar to 3dcluster command in AFNI.
>
> 2) how to generate a table to report all clusters information in a
> stat image in FSL, not all voxel. I can get all voxel coordiates
> using fslmeants -i image --showall.
>
> Any suggestions are appreciated.
> Liang Wang
> --
> Liang Wang, Postdoc
> Woodward Lab
> Department of Psychiatry
> University of British Columbia
> BC Mental Health & Addiction Services
> 938 West 28th Avenue
> Vancouver BC V5Z 4H4
> Telephone: 1-604-875-2000 (ext. 4735)
> Fax: 1-604-875-3871
> Email: [log in to unmask]
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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