Hello,
Can you update to the latest version of FSL ( 5.0.11 ) and let me know if this fixes the randomise crash?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
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Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 19 Mar 2018, at 17:12, Niall Bourke <[log in to unmask]> wrote:
>
> Hello neuroimaging experts,
>
> Problem: running randomise the unpermutated statistic is 0, generating a blank output file
>
> Details:
> I have seen posts relating to setup_masks in the past. I can assume this was under 5.0.8/ as there seems to be differences in the script.
>
> My data n=68, get nice results with the same design and contrasts before including masking.
>
> The following is run:
>
> setup_masks ${root}/designMatrix/demo.mat ${root}/designMatrix/contrast.con ${root}/designMatrix/Lesion `ls ${root}/lesionMasks/*.nii.gz`
>
> Example randomise call:
> randomise -i <input> -o <output> -d /work/nbourke/NODDI/HPC_export/designMatrix/Lesion.mat -t /work/nbourke/NODDI/HPC_export/designMatrix/Lesion.con --vxl=-4 --vxf=/work/nbourke/NODDI/HPC_export/designMatrix/Lesion [other options]
>
>
> Questions:
>
> 1. Could someone clarify the dash before the 4 in --vxl=-4
> 2. The unpermutated statistic is less than 0 -> The contrasts are ok, is this a degrees of freedom? I basically cant get a result this way or is there a work around.
> 3. Is randomise still expecting an separate input rather than the 4D.nii such as the previous version of setup_masks where you would specify --vxl=4,5,..72 vxf=Lesion001, Lesion002, ..
>
>
> Any guidance on why running randomise with the output of setup_masks reduces the results to blank images would be extremely helpful. Many thanks.
