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
>
|