Hi,
It looks like the contrast is a difference between group means,
in which case you shouldn't demean the data ( with -D ). Randomise in
TFCE mode can often get "stuck" when -D is set incorrectly.
Hope this helps
Matthew
> Dear Matthew!
>
> Thanks for that speed answer!
>
> Yes, all there are only 8 generate.e files (and not 136) and they
> all stop after the 2nd perm of the 2nd t-test.
>
> Here are the .con and .mat files.
>
> Just in case, the command was:
> randomise_parallel -i all_FA_skeletonised.nii.gz -o FACTOR3 -m
> FACTOR3_tfce_corrp_tstat1_thresh0.95_bin.nii.gz -d 3FACTOR.mat -t
> 3FACTOR.con -n 5000 -D --T2 -V
>
>
> Thanks so much!
> All the best, Markus
>
>
> 2009/2/5 Matthew Webster <[log in to unmask]>
> Hi Markus,
> Can you send me your design.mat and design.con
> files? Do all the fragments pause at the same iteration?
>
> Many Regards
>
> Matthew
>
> Dear Matthew!
>
> You recently sent me this correction of the the script
> randomise_parallel (see your mail below), in order to correct for
> the problem that there were to many SEED fragments in the folder to
> be deleted properly at the end of the process.
>
> After replacing that lines, I started a new randomise_parallel
> process the 30th January (=7 days ago),
> with 8 contrasts and 32 subjects and I chose 5000 permutations.
>
> What puzzles me now is:
> The process is still running (I have 8 CPU of 3GHz) AND the files
> are not updated any more since the 30 January (c.f. *ls -lrt* for
> the stats folder in attachment).
>
> the **generate.e** files have this warning:
>
> Warning: You have demeaned your data, but at least one design column
> has non-zero mean
>
> the **generate.o** files say this:
>
> Seeding with 8
> Loading Data: ********************************
> Data loaded
> 6.45122e+07 permutations required for exhaustive test of t-test 1
> Doing 37 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
> Starting permutation 14
> Starting permutation 15
> Starting permutation 16
> Starting permutation 17
> Starting permutation 18
> Starting permutation 19
> Starting permutation 20
> Starting permutation 21
> Starting permutation 22
> Starting permutation 23
> Starting permutation 24
> Starting permutation 25
> Starting permutation 26
> Starting permutation 27
> Starting permutation 28
> Starting permutation 29
> Starting permutation 30
> Starting permutation 31
> Starting permutation 32
> Starting permutation 33
> Starting permutation 34
> Starting permutation 35
> Starting permutation 36
> Starting permutation 37
> 6.45122e+07 permutations required for exhaustive test of t-test 2
> Doing 37 random permutations
> Starting permutation 1 (Unpermuted data)
> Starting permutation 2
>
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
> <3FACTOR.con><3FACTOR.mat>
