Hello Henk,
The form of the randomise call below should be fine: it correctly generates "raw" f-stats on test data. -V is the ( deprecated ) verbose option and can safely be ignored. If you want to upload all your input files to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF
we will be able to see if there is a particular problem with your design.
PPheight information is not required by randomise.
Kind regards
Matthew
> Dear FSL-ers,
>
> I tried to run randomise on VBM data with inference turned off, just to quickly check whether our statistical model makes sense.
>
> In the flsvbm/Userguide it is mentioned that the fslvbm_3_proc script runs randomise with inference (generation of p-value maps) turned off, so that it very quickly creates just the raw tstat maps. When looking into the fslvbm3b script created, it seems to call
>
> $FSLDIR/bin/randomise -i ${i}_s${j} -o ${i}_s${j} -m GM_mask -d design.mat -t design.con -V
>
> Because I also want to have raw F-tests I changed this line of code by adding the parameter -f design.fts, but running the command below seems not to work (it runs for hours on the cluster without producing output, also no errors reported).
>
> fsl_sub randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t design.con -f design.fts -V &
>
> Replacing -V with -1 (perform 1-sample group-mean test instead of generic permutation test) does work however. So I was wondering why the -V is here and whether it is necessary. Randomise documentation does not mention -V so what is the functionality?
>
> In addition, is it necessary to add PPheight information to the mat and con files? I have to create these files by hand because the Glm gui is very slow and it took hours to build up the graphics when I tried to model 420 inputs and 20 EVs on the visualization node of our cluster. I am using Windows, so I can't run Glm locally.
>
> Thanks in advance for your help.
>
> Best,
>
> Henk van Steenbergen
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