Hi Xinman,
You're not specifying the output base name in your call to randomise.
Cheers,
Paul
On 11/05/2019, Xinman Liu <[log in to unmask]> wrote:
> Hello, Matthew.
> Thank you for your suggestion.
> I've increased the RAM in VMware to 8GB, but it still doesn't work. So I
> think the problem has something to do with the command line. What do you
> think?
>
> In the terminal it showed:
> [fsluser@localhost stats]$ randomise -i all_FA_skeletonised_left_minus_right
> -m mean_FA_symmetrised_skeleton_mask -d .mat -t .con -1 -v 5 -T
>
>
> Part of FSL (ID: 6.0.1)
> randomise v2.9
>
> Usage:
> randomise -i <input> -o <output> -d <design.mat> -t <design.con> [options]
>
> Compulsory arguments (You MUST set one or more of):
> -i <input> 4D input image
> -o <out_root> output file-rootname
>
> Optional arguments (You may optionally specify one or more of):
> -D demean data temporally before model fitting ( demean model as well if
> required )
> -1 perform 1-sample group-mean test instead of generic permutation test
> -m <mask> mask image
> -d <design.mat> design matrix file
> -t <design.con> t contrasts file
> -f <design.fts> f contrasts file
> -e <design.grp> exchangeability block labels file
> --effective_design <design2.mat> alternative design for determining valid
> permutations
> -q print out how many unique permutations would be generated and exit
> -Q print out information required for parallel mode and exit
> -n <n_perm> number of permutations (default 5000, set to 0 for exhaustive)
> -x output voxelwise corrected p-value images
> --fonly calculate f-statistics only
> -T carry out Threshold-Free Cluster Enhancement
> --T2 carry out Threshold-Free Cluster Enhancement with 2D optimisation
> (e.g. for TBSS data); H=2, E=1, C=26
> -c <thresh> carry out cluster-based thresholding
> -C <thresh> carry out cluster-mass-based thresholding
> -F <thresh> carry out f cluster thresholding
> -S <thresh> carry out f cluster-mass thresholding
> -v <std> use variance smoothing for t-stats (std is in mm)
> -h,--help display this message
> --quiet switch off diagnostic messages
> --twopass carry out cluster normalisation thresholding
> -R output raw ( unpermuted ) statistic images
> --uncorrp output uncorrected p-value images
> -P output permutation vector text file
> -N output null distribution text files
> --norcmask don't remove constant voxels from mask
> --seed <seed> specific integer seed for random number generator
> --tfce_H <H> TFCE height parameter (default=2)
> --tfce_D <H> TFCE delta parameter overide
> --tfce_E <E> TFCE extent parameter (default=0.5)
> --tfce_C <C> TFCE connectivity (6 or 26; default=6)
> --vxl list of numbers indicating voxelwise EVs position in the design
> matrix (list order corresponds to files in vxf option).
> --vxf list of 4D images containing voxelwise EVs (list order corresponds
> to numbers in vxl option).
> --permuteBlocks permute exchangeability blocks. Caution BETA option
> --glm_output output glm information for t-statistics ( unpermuted case only
> )
> --film output stats to simulate the output of film
>
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