Hi - you need to read the README in the FIX distribution - find the section in there on Configuration.
Cheers, Steve.
> On 30 Apr 2015, at 01:17, Sampada Sinha <[log in to unmask]> wrote:
>
> Hello FSL experts
>
> I am trying to run script hcp_fix (my directory for hcp_fix is: hcp_fix/Users/Sampada/Downloads/fix1.06/hcp_fix). My subject folder directory is: Volumes/HCP_Data/fMRI_Resting/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz 200
> When I ran the hcp_fix on the bash terminal it says the following:
>
> rmbp:fix1.06 Sampada$ /Users/Sampada/Downloads/fix1.06/hcp_fix /Volumes/HCP_Data/fMRI_Resting/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz 200
> processing FMRI file rfMRI_REST1_LR with highpass 200
> running highpass
> running MELODIC
> /opt/fmrib/matlab/bin/matlab not found!
> /Users/Sampada/Downloads/fix1.06/call_matlab.sh [-z <mode>] [-o <options>] [-p <path>] [-h <fix path>]
> [-c <mcr path>] [-b <binaries path>] [-l <logfile>]
> {-r <"MATLAB code">|-m <script>|-f <function> [arguments...]}
>
> -z <mode>: This overrides the environment variable
> FSL_FIX_MATLAB_MODE which would otherwise control this.
> 0 = Use compiled MATLAB function specified by
> -m <function name>
> 1 = Use MATLAB - requires -r or -m option
> 2 = Use Octave - requires -r or -m option
> -r <"MATLAB code">: Evaluate the double-quoted MATLAB/Octave
> code. Equivalent to 'matlab -r "MATLAB code"' or
> 'octave --eval "MATLAB code"'
> Ensure that any double quotes in this string are escaped
> with '\'.
> -m <script>:
> -z = 0 or not provided, run as -z = 1
> -z = 1|2 - Run <script> in MATLAB/Octave
> Equivalent to 'matlab \< <script>.m' or 'octave <script>.m'
> -f <function> [arguments]:
> -z = 0 - Call compiled MATLAB <function>
> Arguments to be passed are given in the remainder of the
> command line.
> -z = 1|2 - Run <function> script in MATLAB/Octave
> Equivalent to 'matlab -r "<function>([arguments])"' or
> 'octave --eval "<function>([arguments])"'
> Arguments to be passed are given in the remainder of the
> command line.
> -o <options>: Double quoted list of MATLAB/Octave command line
> options. Defaults to ${FSL_FIX_MLOPTS} or ${FSL_FIX_OCOPTS}
> respectively
> -p <path>: Path to MATLAB/Octave startup script/binary.
> Defaults to: ${FSL_FIX_MATLAB} or ${FSL_FIX_OCTAVE}
> respectively
> -h <path>: Path to folder containing the Fix programs
> -w <path>: Path to FSL MATLAB helper functions, defaults to
> /Applications/fsl/etc/matlab
> -c <mcr path>: Path to MATLAB Compiler Runtime for the version
> of MATLAB Fix was compiled under. Defaults to ${FSL_FIX_MCRROOT}
> -b <compiled path>: Path to the folder containing the compiled MATLAB
> functions. Defaults to ${FSL_FIX_MLCDIR}
> -l <logfile>: Append console and error output to <logfile>\n
> running FIX
> FIX Feature extraction for Melodic output directory: rfMRI_REST1_LR_hp200.ica
> create edge masks
> run FAST
> registration of standard space masks
> extract features
> /opt/fmrib/matlab/bin/matlab not found!
> /Users/Sampada/Downloads/fix1.06/call_matlab.sh [-z <mode>] [-o <options>] [-p <path>] [-h <fix path>]
> [-c <mcr path>] [-b <binaries path>] [-l <logfile>]
> {-r <"MATLAB code">|-m <script>|-f <function> [arguments...]}
>
> -z <mode>: This overrides the environment variable
> FSL_FIX_MATLAB_MODE which would otherwise control this.
> 0 = Use compiled MATLAB function specified by
> -m <function name>
> 1 = Use MATLAB - requires -r or -m option
> 2 = Use Octave - requires -r or -m option
> -r <"MATLAB code">: Evaluate the double-quoted MATLAB/Octave
> code. Equivalent to 'matlab -r "MATLAB code"' or
> 'octave --eval "MATLAB code"'
> Ensure that any double quotes in this string are escaped
> with '\'.
> -m <script>:
> -z = 0 or not provided, run as -z = 1
> -z = 1|2 - Run <script> in MATLAB/Octave
> Equivalent to 'matlab \< <script>.m' or 'octave <script>.m'
> -f <function> [arguments]:
> -z = 0 - Call compiled MATLAB <function>
> Arguments to be passed are given in the remainder of the
> command line.
> -z = 1|2 - Run <function> script in MATLAB/Octave
> Equivalent to 'matlab -r "<function>([arguments])"' or
> 'octave --eval "<function>([arguments])"'
> Arguments to be passed are given in the remainder of the
> command line.
> -o <options>: Double quoted list of MATLAB/Octave command line
> options. Defaults to ${FSL_FIX_MLOPTS} or ${FSL_FIX_OCOPTS}
> respectively
> -p <path>: Path to MATLAB/Octave startup script/binary.
> Defaults to: ${FSL_FIX_MATLAB} or ${FSL_FIX_OCTAVE}
> respectively
> -h <path>: Path to folder containing the Fix programs
> -w <path>: Path to FSL MATLAB helper functions, defaults to
> /Applications/fsl/etc/matlab
> -c <mcr path>: Path to MATLAB Compiler Runtime for the version
> of MATLAB Fix was compiled under. Defaults to ${FSL_FIX_MCRROOT}
> -b <compiled path>: Path to the folder containing the compiled MATLAB
> functions. Defaults to ${FSL_FIX_MLCDIR}
> -l <logfile>: Append console and error output to <logfile>\n
> No valid training file specified
> No valid labelling file specified
> rmbp:fix1.06 Sampada$
>
> I don't have matlab installed since FIX 1.06 version said it doesn't need, however apart from FIX 1.06 I have also installed matlab compiler, R statistical package and other installation (using README) with others (fortran, tcltk-8.5.5-x11.pkg.
>
>
> Will you please let me know where I am going wrong? Appreciate all your help!
>
> Thanks and regards,
>
> Sampada
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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