SPM/Octave

GNU Octave

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

• 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

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

SPM is not supported under Octave and there is a number of known limitations (especially regarding the 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 (4.2).

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

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

Requires changes in SPM

• 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.

Requires changes in Octave

• Line continuation "..." does not ignore anything that appears after it, unless there is a comment sign % (MATLAB does). fixed
• strrep.m works on strings but not cell arrays. fixed
• 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','.') fixed
• 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 filesep in addpath/rmpath fixed
• a='a';b={};c=cellfun(@(x)strcmp(a,x),b); crashes with Octave (devel, not 3.2.4) while MATLAB returns c=[]. fixed
• Same error with b=get(findobj(0,'Tag','xxx'),'a') which should return [], i.e. problem with functions that return empty output. fixed
• save.m (and perhaps load.m) have trouble with MATLAB binary MAT-format. (when some variables are not double precision (e.g. clear a;a.field1=single(1);save a.mat a -v6;load a.mat crashes on Octave dev ("error: load: invalid element type = 0") fixed). fixed
• dialog, errordlg, helpdlg, inputdlg, listdlg, msgbox, warndlg do not exist in Octave.
• gco.m now exists in Octave but creates a figure if none exists. fixed.
• fcnchk.m does not exist in Octave (can usually be replaced by str2func.m)
• 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. fixed
• Several problems with hierarchical classes. fixed, fixed, fixed, fixed, fixed, fixed, in progress
• Assignment error with non-preallocated 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);). fixed
• str2num(',1,1') returns [1 1] in MATLAB and [] in Octave. fixed
• 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 (get([],'x')). fixed
• Compatibility: save with empty variable names. fixed
• Test on fileparts input argument. 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. fixed
• [[];{'a'}] returns {[];'a'} instead of {'a'}, won't fix
• Empty struct struct([]) not preserved when saved in a MAT-file. fixed
• Problem in regexprep with backslash escape character. fixed
• Segmentation fault with [B,C]=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. fixed
• mkoctfile does not recognize argument -outdir.
• desktop function does not exist, particularly useful for calls desktop('-inuse'). fixed
• Compilation with SuiteSparse 3.2 fails. fixed
• undefined symbol: mexCallMATLAB. fixed
• Segmentation fault with clf.m test. fixed
• W specifier in fopen does not work. fixed
• Parser oddity with if statements. fixed
• 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., fixed
• Compilation error yylex was not declared in this scope., fixed
• Compilation failure due to openGL. fixed
• -depth argument in findobj., fixed
• evalc is not defined. fixed
• io64.h is not defined, in progress.
• save function handle variables in MATLAB's binary data format, in progress
• Support of close all force., fixed
• warning in findobj when using regexp., fixed
• Printing a figure not containing axes. fixed
• Error following an error in a callback of a uimenu. fixed
• SelectionType open for double-click non available (Qt-only). fixed
• hgload can't open MATLAB figures, in progress
• Difference with figure/uicontrol between Octave and MATLAB, in progress
• Segmentation fault when loading a MAT-file containing a function_handle to a subfunction, in progress
• Behaviour of figure property ToolBar when set to auto. fixed
• Properties of a popupmenu uicontrol. fixed
• Callback execution of an edit uicontrol. fixed
• Mouse interaction with image objects don't work in fltk toolkit, in progress
• Property value of checkbox uicontrol. fixed
• Changing the style of a uicontrol after creation, in progress
• Display of popupmenu uicontrol (Qt) in progress
• Mouse click callbacks of a listbox uicontrol, in progress
• Interpretation of cell array in String property of a text uicontrol. fixed
• Incorrect output in textscan/strread with trailing delimiter. fixed
• Failure to exit when running Octave in --no-gui mode. fixed
• Freeze with drawnow. fixed
• Print options: -noui, -painters, -opengl. fixed
• Reset submenus of a uicontextmenu, in progress
• Legend object printed below lines in plot, in progress
• Order of uimenus. fixed
• CreateMode argument for msgbox/errordlg/warndlg. fixed
• Error no method for 'scalar struct = scalar' fixed
• Print does not preserve multiline text and TeX markup in progress
• Removing a context menu. fixed
• Case-sensitive listdlg's SelectionMode values. fixed
• Image display in a 3D view, in progress
• Issues with copy to clipboard. fixed
• Error base_graphics_object::get_properties: invalid graphics object, in progress
• Visible property of a uicontextmenu fixed
• make attempts to build libgui even with --disable-gui. fixed
• function localfunctions not implemented. fixed
• function import not implemented, in progress
• Access to object arrays, in progress
• Loading a function handle from a MAT-file, in progress
• Segmentation fault with missing warning state "all". fixed
• corrcoef is missing, in progress
• Third output of uiputfile undefined when user presses Cancel. fixed