Hi - yes, this sounds familiar and I thought was fixed - are you
definitely running the latest sub-version of FSL / randomise patch?
Cheers.
On 30 Nov 2009, at 01:09, Agatha Lenartowicz wrote:
> Hi all ~
>
> I have recently conducted a bunch of masked (i.e., ROI) analyses
> using randomise (and randomise_parallel). I observed that the
> program got *stuck* every now and then - without error output. On
> the cluster the submitted job was reported "running", and when
> running locally the program would get stuck at the second
> permutation (i.e., first attempt to permute original input). All of
> my log files showed that all was well... and yet, no new files were
> being produced.
>
> Since this typically occurred when the mask (-m mask.nii.gz) was
> anatomically small - I wondered whether the problem was that there
> were no non-zero statistics in the map which was somehow confusing
> the script. It turned out that this was true in all the cases in
> which I checked.
>
> So... I don't know if I've diagnosed correctly but there is
> definitely something funky going on, and which can force randomise
> to a halt without producing error messages.
>
> The command I used is below - if you'd like to check out my inputs
> I'd be happy to upload them...
> # sge qsub randomise_parallel -i ${DATA_PATH} \
> # -o ${CONTRAST}_${ROI_NAME[ROI]}_pos \
> # -m ${MASK_PATH}/${ROI_NAME[ROI]}.nii.gz \
> # -1 \
> # -v 8 \
> # -T \
> # -V
>
> Best ~
> Agatha
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> Agatha Lenartowicz, Ph.D.
> Post Doctoral Scholar
> Laboratory of R.A. Poldrack
> www.poldracklab.org
>
> UCLA Department of Psychology
> 1285 Franz Hall, Box 951563
> Los Angeles, CA, 90095-1563
>
> http://alenarto.bol.ucla.edu/
>
>
>
>
> On Oct 28, 2008, at 7:04 PM, Koene Van Dijk wrote:
>
>> For who is looking for the file "colourbar.nii.gz" that was
>> mentioned in
>> this thread. It is still attached to the post by Mark Jenkinson on
>> this
>> subject "fslview LUT color bar" (09-01-2008)
>>
>> This is the location of the attachment:
>> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A3=ind0801&L=FSL&E=base64&P=458288&B=--Apple-Mail-3-372292755&T=application%2Fx-gzip;%20name=%22colourbar.nii.gz%22&N=colourbar.nii.gz&attachment=q
>>
>> Thanks Mark, because I used it again today,
>>
>> Cheers,
>> Koene
>
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