Good - now you need to run with a 'normal' number of iterations - at
least 500, if not 5000 to be even more accurate with your p-values.
Cheers.
On 18 Aug 2009, at 18:44, Miguel Burgaleta wrote:
> Hi Steve - Now I am getting the output after setting -n 20. Most
> likely the problem was that the job got mistakenly killed?
>
> Thanks for your help.
>
> Best,
> Miguel
>
>
> On Mon, Aug 17, 2009 at 11:21 PM, Steve Smith <[log in to unmask]>
> wrote:
> Hi - try adding "-n 20" to limit the number of permutations whilst
> you are sorting this out. Does it appear to go through the
> permutations and claim to save any output? Are you sure you looked
> for output in /ifs/four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/4D/ ?
>
> Cheers.
>
>
>
>
> On 18 Aug 2009, at 00:03, Miguel Burgaleta wrote:
>
> Thanks Steve -- Hm, I do have permissions in that folder, but got no
> output nor error message.
> Do you see something weird in the command?:
>
> ***************** quoting *************************
> randomise -i /ifs/four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/4D/
> FA_4D.nii.gz -o /ifs/four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/4D/
> TvalFA_ -d /ifs/four_d/MIGUEL/FULL_SAMPLE/STATS/DesignMatrices/
> randomise/DM_randomise_IQ_speed.mat -t /ifs/four_d/MIGUEL/
> FULL_SAMPLE/STATS/DesignMatrices/randomise/Contrast.con -m /ifs/
> four_d/MIGUEL/FULL_SAMPLE/IMAGES_4STATS/mask_WM_4stats.img -T
>
> ******************************************************
>
> Miguel
>
>
>
>
>
> On Mon, Aug 17, 2009 at 9:27 AM, Steve Smith <[log in to unmask]>
> wrote:
> Hi - the randomise output is determined by the output filename you
> give it - after "-o" on the command - if you don't specify a
> directory name as part of this option the output will be in the
> directory you run randomise is. If this directory is not writable by
> you I suppose there may be no output.
>
> Cheers.
>
>
>
> On 17 Aug 2009, at 18:22, Miguel Burgaleta wrote:
>
> Thanks Steve!
> I was somehow expecting the /Custom line to specify the path for the
> output... If not, where should I look at? randomise seems to run ok
> but I am unable to find the output!
>
> Best,
> Miguel
>
> On Mon, Aug 17, 2009 at 2:54 AM, Steve Smith <[log in to unmask]>
> wrote:
> HI, Custom is for historical reasons - not used generally now.
>
> PPheight is best left in, as it may be used by some programs - it
> should be the peak-peak height of each regressor.
>
> Cheers.
>
>
>
> On 14 Aug 2009, at 21:34, Miguel Burgaleta wrote:
>
> Hello,
>
> I am trying to set up the design.mat file in order to run randomise.
> However, I have 2
> questions about the meaning of some of the lines in the file and I
> was unable to find an
> answer by browsing your archives.
>
> 1. What does the /Custom line means?
> 2. Is it true that I can just remove the /PPheight line?
>
> Thanks in advance for your time!
>
> Cheers,
> Miguel
>
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
>
>
> ---------------------------------------------------------------------------
> 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
---------------------------------------------------------------------------
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