2008/11/25 Steve Smith <[log in to unmask]>

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
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--
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
---------------------------------------------------------------------------