 |
 |
Hi, On 17 Jul 2008, at 02:10, Kenneth Qiu wrote: > Hi Steve, > > Thank you very much for your reply. Will F-tests using TFCE be > available in the next release? Yes - very soon. Cheers. > I can see clusters from both images using two lut, it is just that > they don't match and actually are very different from each other. > "Cluster" shows 33 clusters with 1-p > 0.95 and the largest one has > 6825 voxels. I will try using a subset of the data and see whether > it produces similar result. > > > > Best, > Deqiang > > > On Thu, Jul 17, 2008 at 1:49 AM, Steve Smith <[log in to unmask]> > wrote: > Hi, > > Sorry, yes TFCE and F-tests have not yet been combined in randomise, > apologies. > > Were the cluster-based F-test thresholdings different in extent or > just were some missing from the maxc output? If the latter it may > just be that they had P=1 so didn't show up? If that doesn't solve > it then maybe send the images to Matthew to debug? > > Cheers, Steve. > > > > > On 16 Jul 2008, at 02:52, Kenneth Qiu wrote: > > Dear All, > > I'm using fsl-4.0.4-centos5_64 on Ubuntu 7.10 (64 bits) - the Gutsy > Gibbon installed on a machine with intel core 2 Duo. > > I am trying to study DTI -reading ability correlation with TBSS. > Basically, I have three groups of subjects with different age and > the age spans within each groups are small. In order to find regions > of the brain whose FA values are correlated with reading scores, I > use the following design, where G1,2,3 represent the three groups > and R1,2,3 are reading scores demeaned within each group. > > reading.mat > > G1 G2 G3 R1 R2 R3 > > Sub1_1 1 0 0 a1 0 0 > Sub1_2 1 0 0 a2 0 0 > ... > Sub2_1 0 1 0 0 b1 0 > Sub2_2 0 1 0 0 b2 > ... > Sub3_1 0 0 1 0 0 c1 > Sub3_2 0 0 1 0 0 c2 > .... > > reading.con: > > /ContrastName1 EReadGrp1 > /ContrastName2 EReadGrp2 > /ContrastName3 EReadGrp3 > /NumWaves 6 > /NumContrasts 3 > /PPheights 4.500000e+01 1.130000e+02 5.400000e+01 > /RequiredEffect 3.955 2.500 3.995 > > /Matrix > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 > 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 > 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 > > > reading.fts: > /NumWaves 3 > /NumContrasts 1 > > /Matrix > 1 1 1 > > > Since it is possible that the same brain region may having different > correlate with reading among individual group, I decided to use F > test. As Steve and Tom suggest TFCE is sensitive but slower, I > decided to give it a try with small #perm. I used randomise -i fa_4d > -m mean_FA_skeleton_mask -o reading -d readign.mat -t reading.con -f > reading.fts -T -n 50 -V . I didn't see any tfce for F test but only > for the three t contrasts. Is TFCE not yet implemented for F test? > > I then turned to cluster-based inference using randomise -i fa_4d -m > mean_FA_skeleton_mask -o reading -d readign.mat -t reading.con -f > reading.fts -F 12 -n 50 -V. I chose 12 as threshold based on my > observation of a previous run of randomise . To my surprise, the > cluster from reading_maxc_fstats did not match what I got by > thresholding reading_fstats manually in fslview. And I think the > cluster extents should be identical according to my understand of > clustered based inference. Could anyone please help? Thank you very > much! > > Sorry for the lengthy email, I try to give enough information for > people to diagnose. > > Best, > Deqiang > University of Hong Kong > > > > > --------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------- > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------