# SPM/Octave

From Wikibooks, open books for an open world

< SPM

## GNU Octave[edit]

GNU Octave is a high-level language that is mostly compatible with MATLAB. It is free open source software under the terms of the GNU General Public License.

### Octave[edit]

- Octave website: http://www.gnu.org/software/octave/
- Octave project: http://hg.savannah.gnu.org/hgweb/octave/
- Octave Help mailing list: https://lists.gnu.org/mailman/listinfo/help-octave
- Octave Maintainers mailing list: https://lists.gnu.org/mailman/listinfo/octave-maintainers
- Octave bug tracker: http://savannah.gnu.org/bugs/?group=octave
- Octave-Forge: http://octave.sourceforge.net/
- GNU Octave and reproducible research by John W. Eaton

### MATLAB/Octave compatibility[edit]

GNU Octave is mostly compatible with MATLAB:

- http://wiki.octave.org/Compatibility
- http://wiki.octave.org/FAQ#Porting_programs_from_Matlab_to_Octave
- http://en.wikibooks.org/wiki/MATLAB_Programming/Differences_between_Octave_and_MATLAB
- http://homepages.inf.ed.ac.uk/imurray2/compnotes/octave_matlab.html

Compatibility status from other neuroimaging MATLAB packages:

- EEGLAB: http://sccn.ucsd.edu/wiki/EEGLAB_and_Octave
- FieldTrip: http://fieldtrip.fcdonders.nl/faq/can_i_use_octave_instead_of_matlab
- Psychtoolbox: http://psychtoolbox.org/

## Current status for SPM/Octave compatibility[edit]

SPM is **not** supported under Octave and there is a number of known limitations (no graphical interface and no batch system) but feel free to contact fil.spm@ucl.ac.uk if you are interested. In most situations, the standalone version of SPM might be a sufficient alternative.

You need to use latest version of SPM12 and GNU Octave (3.8).

For compilation of the MEX files for Octave, run the following:

cd /home/login/spm12/src make distclean PLATFORM=octave make PLATFORM=octave && make install PLATFORM=octave

### How to contribute[edit]

You can contribute to improve the support of SPM on GNU Octave in several ways:

*Report bugs:*using the development version of Octave, report problems you encounter when using SPM to SPM or Octave developers. Make sure to only report a bug in Octave when it's something that should not be fixed in SPM instead. Try to isolate the problem as much as possible.*Propose patches*in Octave for bugs from the list below that have not been fixed yet.*Contribute financially*to the Octave community.

## Compatibility issues observed so far in SPM with Octave[edit]

### Requires changes in SPM[edit]

- Compilation of MEX files: use
**"mkoctfile --mex"**and the MEX-file extension is ".mex" on all platforms. - It is not possible to create a
**function handle**with a function name that does not exist (eg, x = @sdlkjfhg fails, see this). **do**is a reserved keyword in Octave (for a do-until loop) so cannot be used as variable name.**disp**should be called instead of**display**for standard variables (in OO programming).**builtin('display',obj)**does not work on user-defined objects (MATLAB returns 'classname object: x-by-y', i.e. it calls disp.m).**class**can only be called from the class constructor (and not in any other method function) (class(obj,'myclass') => myclass(obj)).- The short-circuit
**&&**and**||**operators should be used in if statements, instead of binary operators & and |. This is reported by MLINT. - MEX files should include "mex.h" but not
**"matrix.h"**, see this **cd**does not return current directory in Octave (unlikely to change, see this thread). Call**pwd**beforehand instead.~~Line continuation "~~fixed**...**" does not ignore anything that appears after it, unless there is a comment sign**%**(MATLAB does).

### Requires changes in Octave[edit]

fixed**strrep.m**works on strings but not cell arraysfixed**isdeployed.m**does not exist (function X=isdeployed, X=false;)fixed**textscan.m**,**strread.m**and**textread.m**do not exist (in 3.2.4; available in devel, see this and this). Note that in MATLAB, textscan should be preferred and replace strread and textread. The devel function crashes on*textscan('aaa.bbb','%s','delimiter','.')*~~A subfunction of a private class method does not access fields directly (i.e. it's a step further from this) and calls subsref/subsasgn instead.~~fixed**which.m**does not support the -ALL option (see this). in progress~~trailing~~fixed**filesep**in**addpath**/**rmpath**fixed*a='a';b={};c=*crashes with Octave (devel, not 3.2.4) while MATLAB returns c=[].**cellfun**(@(x)strcmp(a,x),b);~~Same error with~~fixed*b=*which should return [], i.e. problem with functions that return empty output.**get**(findobj(0,'Tag','xxx'),'a')(**save.m**(and perhaps**load.m**) have trouble with MATLAB binary MAT-format~~when some variables are not double precision (e.g.~~fixed). fixed*clear a;a.field1=single(1);save a.mat a -v6;load a.mat*crashes on Octave dev ("error: load: invalid element type = 0")**dialog, errordlg, helpdlg, inputdlg, listdlg, msgbox, warndlg**do not exist in Octave.fixed.**gco.m**now exists in Octave but creates a figure if none exists.**fcnchk.m**does not exist in Octave (can usually be replaced by**str2func.m**)fixed**isequal.m**does not work with objects (*error: find: wrong type argument `class', __isequal__.m at line 147*).fixed**logm**(eye(3)) crashes, MATLAB returns zeros(3).fixed**logm**sometimes returns complex numbers.fixed**mat2str**fails on logical inputs- Several problems with hierarchical classes. fixed, fixed, fixed, fixed, fixed, fixed, in progress
~~Assignment error with non-preallocated~~fixed**sparse**matrices (*clear a; a(1,:)=sparse(1,3,1,1,3);*returns*A(I,J,...) = X: dimensions mismatch*.fixed**tic/toc**do not handle input/output arguments as in MATLAB (*tStart=tic; any_statements; tElapsed=toc(tStart);*).**str2num**(',1,1') returns [1 1] in MATLAB and [] in Octave, won't fix~~Objects not converted as structure when loaded from a MAT-file if class definition is not in path.~~fixed~~Accessing graphics object properties from an empty handle displays obscure warning (~~fixed*get([],'x')*).fixed**nargchk**(1,1,1,'struct') returns a 1x1 struct with no fields in Octave and a 0x1 struct with fields*message*and*identifier*in MATLAB.returns**[[];{'a'}]***{[];'a'}*instead of*{'a'}*, won't fix~~Empty struct~~fixed**struct([])**not preserved when saved in a MAT-file.~~Problem in~~fixed**regexprep**with**backslash**escape character.~~Segmentation fault with [B,C]=~~fixed**chol**(-speye(3))fixed**mwSignedIndex**is not defined => typedef int mwSignedIndex;fixed**cell arrays of cell arrays**as saved by matlabbatch are not parsed properly with Octave.**mkoctfile**does not recognize argument**-outdir**.fixed**desktop**function does not exist, particularly useful for calls**desktop('-inuse')**.~~Compilation with~~fixed**SuiteSparse 3.2**fails.~~undefined symbol:~~fixed**mexCallMATLAB**.fixed**W**specifier in fopen does not work.~~Parser oddity with~~fixed**if**statements~~Problem with mxArray in MEX files~~fixed- Parse error with local functions in classdef files, in progress
~~ind2rgb does not handle float inputs in the same way than MATLAB.~~fixed- Invalid conversion from string to real scalar with %c, in progress
~~Compilation error "‘yylex’ was not declared in this scope"~~, fixed- "-depth" argument in findobj, in progress
**io64.h**is not defined.

### Undecided yet[edit]

- mkoctfile's option to define output file name is "-o" or "--output" while mex's option is "-output". If used, no file extension ('.mex') is appended.
- MEX object files "*.o" are not automatically deleted after compilation (they are with MATLAB's mex).
**computer.m**returns different strings than on MATLAB (PCWIN, GLNX86, PCWIN64, GLNXA64, MACI64), e.g. x86_64-unknown-linux-gnu.**load.m**and**save.m**automatically add a*.mat*file extension if not provided with MATLAB (Octave doesn't).- Octave buffers output, which can be blocking.
**fflush(stdout)**or page_screen_output has to be used.

### Miscellaneous[edit]

**exist('OCTAVE_VERSION','builtin')**can be used to detect if running in Octave or MATLAB.