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Hi Reza, Thanks for the response! By the way I meant to be talking about L1 in my original email, and not MD. I checked the mask and it was OK, but I recreated it anyway and tried running with the --T2 options specified through -T like you suggested below. Same thing...Randomise with TFCE gets stuck on permutation 2. Out of curiosity I tried running some other combinations and got some strange results: - MD: Runs fine with the 0.95 thresholded 1-p mask (made from the original FA contrast - see original message). - L1: Does not run with the 0.95 thresholded 1-p mask (hangs at permutation 2 of tstat1). Does run through properly when I threshold the mask at 0.949 or anything lower. - RD (L2+L3)/2: Does not run with the 0.95 thresholded 1-p mask (hangs at permutation 2 of tstat*2*). Does run through properly when the mask is thresholded at 0.89 (but not higher). All of these run fine if I use the full mean_FA_skeleton mask, or try one of the other modes (cluster-mass). I've also tried recreating the data files with the tbss_non_FA script, but no improvement with that either. I do, however, recreate the exact same problems when I try to run the analyses on my local machine (x86 64bit MacPro) instead of our cluster (x86 64bit Linux running SGE). Any ideas? Is there any way I can get additional debugging output from randomise? As it is, things just silently hang on "permutation 2". Thanks again for the help! John On Mon, 27 Oct 2008 22:12:23 +0000, Reza Salimi <[log in to unmask]> wrote: >Hi John, >it shouldn't be like that, >could you please check your mask and if it's allright, just rerun the >analysis with -T option >(with --tfce_H=2 --tfce_E=1 --tfce_C=26)??? >thanks, Reza > > > >On Mon, Oct 27, 2008 at 9:51 PM, John Colby <[log in to unmask]> wrote: > >> Hello all, >> >> I'm doing a 50 subject TBSS project in FSL 4.1.0 and was hoping to use a >> TFCE mode >> FWE-corrected p<0.05 significant region from the whole-brain FA analysis as >> a mask for a >> subsequent investigation looking at MD. When doing this, randomise runs >> properly in the - >> C cluster mass mode, but simply hangs on permutation 2 when I try to run it >> in the --T2 >> TFCE mode. >> >> When I expand my mask to p<0.06 or higher, however, --T2 TFCE also works >> fine. Which >> is why I'm curious, is there a "minimum number of voxels" requirement wired >> into TFCE? >> >> Thanks! >> >> John Colby >> >> MD/PhD student >> Developmental Cognitive Neuroimaging Lab >> David Geffen School of Medicine at UCLA >> >> Commands/outputs: >> >> Masks generated like: >> jcolby>> fslmaths FA_tfce_corrp_tstat2 -thr 0.95 -bin >> FA_tfce_corrp_tstat2_95_bin >> >> p<0.05 mask (186 voxels): >> jcolby>> randomise -i all_MD_skeletonised -o MD -m >> FA_tfce_corrp_tstat2_95_bin -d >> design.mat -t design.con -n 1000 --T2 -V >> Loading Data: ***************************************************** >> Data loaded >> 7.52118e+21 permutations required for exhaustive test of t-test 1 >> Doing 1000 random permutations >> Starting permutation 1 (Unpermuted data) >> Starting permutation 2 >> (hangs here forever...) >> >> p<0.06 mask (625 voxels): >> jcolby>> randomise -i all_MD_skeletonised -o MD -m >> FA_tfce_corrp_tstat2_94_bin -d >> design.mat -t design.con -n 1000 --T2 -V >> Loading Data: ***************************************************** >> Data loaded >> 7.52118e+21 permutations required for exhaustive test of t-test 1 >> Doing 1000 random permutations >> Starting permutation 1 (Unpermuted data) >> Starting permutation 2 >> Starting permutation 3 >> Starting permutation 4 >> Starting permutation 5 >> Starting permutation 6 >> Starting permutation 7 >> Starting permutation 8 >> Starting permutation 9 >> Starting permutation 10 >> Starting permutation 11 >> Starting permutation 12 >> Starting permutation 13 >> (etc..., finishes properly) >> > > > >-- >G. Salimi-Khorshidi, >D.Phil. Student, Dept. of Clinical Neurology, University of Oxford. >[log in to unmask] http://www.fmrib.ox.ac.uk/~reza >FMRIB Centre, John Radcliffe Hospital, >Headington, Oxford, OX3 9DU >Tel: +44 (0) 1865 222466 Fax: +44 (0)1865 222717 >