I think I can guess what's happening - there's a line in randomise
that estimates the TFCE height increment ("delta") as a one hundredth
of the maximum tstat value - so it's possible that if you have a very
restricted input mask, this might possibly end up as zero, in which
case the TFCE height looping might run forever.
We will check on that and let you know next week; but, for now, I
suspect that if your mask is VERY small then you don't need TFCE
anyway, and you could just run with normal corrected voxelwise p-values.
Cheers.
On 8 Nov 2008, at 00:10, John Colby wrote:
> 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
>>
>
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
