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Hi - although this is sometimes done in reporting studies, I'm afraid it's not really valid as a way of controlling for multiple comparisons across voxels. If you didn't find any significant clusters, have you tried using TFCE (i.e. the --T2 option)? If none of these work, the only other way to 'boost' significance is to limit the search space (randomise mask) to only those areas of the brain/skeleton that you honestly are considering looking for results in. Cheers. On 25 Nov 2008, at 09:08, liang wang wrote: > Dear Steve, > > Thanks for your help. > At the initial stage, I attempted to use 0.95 to threshold the > _tfce_corrp_tstat_ or _vox_corrp_tstat images. however, no > significant results could survive in this situation. Accordingly, I > just used more conservative value (0.995) to threshold the _vox_p > image and got an uncorrected image. As an additional safeguard > against false positives, we only retained clusters larger than 10 > voxels in size. Do you think if this step is rationable. > > Many thanks, > Liang Wang > > > 2008/11/25 Steve Smith <[log in to unmask]> > 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] > > > --------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------- > > > > -- > 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] --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------