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Dear Richard,

The input file to randomise needs to be a 4D image - not a list of 3D images.
You can use fslmerge to create a 4D image from a list of 3D images.

You also should not include the characters "<" and ">" in your actual command.
These are listed in the help/usage to indicate a placeholder for a compulsory argument and that the whole thing needs to be replaced by an actual word/name.
I recommend that you read the basic UNIX tutorial at:  http://www.fmrib.ox.ac.uk/fslcourse/unix_intro/
and the last few slides in the Introductory lecture from the FSL course: http://www.fmrib.ox.ac.uk/fslcourse/lectures/intro.pdf
I've included the text from the single most relevant slide below.

Most importantly, if you are trying to run VBM, then you shouldn't be passing in the original images anyway.  You need to follow the instructions at: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM/UserGuide

All the best,
Mark



FSLUTILS
misc command-line programs
• Each command-line tool provides a usage message is run with 
no arguments (i.e. options/inputs).  For example:
$ fslsplit
Usage: fslsplit <input>
       fslsplit <input> [output_basename] [-t/x/y/z]
       -t : separate images in time (default behaviour)
       -x : separate images in the x direction
       -y : separate images in the y direction
       -z : separate images in the z direction
• Compulsory arguments look like <this>
• Optional arguments look like [this]
- A set of options looks like [this/that/other] where only one 
should be used in any command
• Any “double minus” args need an equals sign (with no spaces)
    e.g.   fsl_tsplot -i inputfile -o outputfile --start=2


On 21 Nov 2012, at 07:38, Richard Bethlehem <[log in to unmask]> wrote:

Hi Everyone,

I'm having some issues creating a design matrix for VBM, when I use the randomise function it just lists all the option so clearly I'm mistyping something:

bash-3.2$ randomise -i <Con_pp001_t1MRI.nii Con_pp002_t1MRI.nii Con_pp003 Con_pp004_t1MRI.nii Con_pp005_t1MRI.nii Con_pp006_t1MRI.nii Con_pp007 Con_pp008_t1MRI.nii Con_pp009_t1MRI.nii Con_pp010_t1MRI.nii Con_pp011_t1MRI.nii Con_pp013_t1MRI.nii Pat_pp101_t1MRI.nii Pat_pp102_t1MRI.nii Pat_pp103_t1MRI.nii Pat_pp104_t1MRI.nii Pat_pp105_t1MRI.nii Pat_pp106_t1MRI.nii> -o </Users/richard/T1_VBM/> -d design.mat -t design.con -n 500 -D -T

Would be great if anyone could help me out here.

Best,

Richard