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
---------------------------------------------------------------------------
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