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: https://octave.org/ 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 GitHub: https://github.com/gnu-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/FAQ#Differences_between_Octave_and_Matlab https://en.wikibooks.org/wiki/MATLAB_Programming/Differences_between_Octave_and_MATLAB http://wiki.octave.org/Compatibility Compatibility status from other neuroimaging MATLAB packages: EEGLAB: https://sccn.ucsd.edu/wiki/Running_EEGLAB_on_Octave FieldTrip: http://www.fieldtriptoolbox.org/faq/can_i_use_octave_instead_of_matlab/ Psychtoolbox: http://psychtoolbox.org/ Current status for SPM/Octave compatibility SPM is currently not officially supported under Octave but many modules are effectively compatible. Feedbacks about further evaluation and validation are very welcome. In most situations, the standalone version of SPM might be a sufficient alternative. Feel free to contact fil.spm@ucl.ac.uk if this is something you are interested in. You need to use the latest versions of SPM12 and GNU Octave (7.3). Compilation For compilation of the MEX files for Octave, run the following: <nowiki> cd /home/login/spm12/src make PLATFORM=octave make PLATFORM=octave install </nowiki> An all-in-one Octave script to download, configure and install SPM in the current directory is as follow (to be typed at the Octave prompt): <nowiki> %% Store current working directory cwd = pwd; %% Download SPM12 r7771 unzip ("https://github.com/spm/spm12/archive/r7771.zip", cwd); %% Patch SPM12 urlwrite ("https://raw.githubusercontent.com/spm/spm-octave/main/spm12_r7771.patch", "spm12_r7771.patch"); system ("patch -p3 -d spm12-r7771 < spm12_r7771.patch"); %% Compile MEX files cd (fullfile (cwd, "spm12-r7771", "src")); system ("make PLATFORM=octave"); system ("make PLATFORM=octave install"); %% Add SPM12 to the function search path addpath (fullfile (cwd, "spm12-r7771")); cd (cwd); %% Start SPM12 spm </nowiki> 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 between SPM and Octave Requires changes in SPM Compilation of MEX files: use "mkoctfile --mex" and the MEX-file extension is ".mex" on all platforms. 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 It is not possible to create a function handle with a function name that does not exist (eg, x = @crash fails). fixed 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. in progress 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. fixed 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. fixed Third output of uiputfile undefined when user presses Cancel. fixed MEX object files "*.o" are not automatically deleted after compilation (they are with MATLAB's mex). fixed Octave buffers output, which can be blocking. fflush(stdout) or page_screen_output has to be used. pager disabled by default in 4.4 /usr/X11R6/lib/libGL.so: could not read symbols on Suse 64 bits. fixed CHOLMOD_NOT_POSDEF was not declared in this scope. fixed sortrows/sort: only cell arrays of character strings may be sorted error. fixed Error in concatenation of classdef objects, in progress Restore window button does not trigger a repaint event for its content. fixed ginput doesn't correctly process shift/ctlr/alt key combinations.fixed GUI Command Window could support syntax highlight, in progress Ctrl+C doesn't interrupt and causes SIGABRT at exit. fixed mxCreateNumericArray with zero size. fixed Build error with mx-cdm-dm.cc. fixed linspace() incompatibility with Matlab when N < 2. fixed Make display of coordinates in figure's status bar optional. fixed Crash when uicontrol's callback returns an error. fixed Refresh when using waitfor. fixed ButtonDownFcn callback of an image. fixed run behaves differently from Matlab on function m-files. fixed doc build fails with texi2dvi/texi2pdf errors on Ubuntu 14.04. fixed Figure handle input argument for close(...,'force'). fixed "parse error" error message in GUI callbacks. fixed delete(allchild(fig)) in a "deletefcn" callback raises error. fixed missing getframe function. fixed Special characters in uicontrol's string. fixed prefdir should not be a private function. fixed Help menu of Qt figures. fixed Detection of Qscintilla libraries. fixed Root graphics property "MonitorPositions" not fully implemented, in progress Default settings with uicontrols. fixed Segmentation fault with Qt figures. fixed uicontrols extent is incorrect, in progress mexCallMATLABWithTrap not implemented. fixed mxSetDimensions for cell arrays. fixed realpow: produced complex result. fixed Cannot set breakpoints in subfunctions from GUI editor when not using "endfunction" keyword, in progress Missing MEX function mxArrayToUTF8String, in progress Backgroundcolor ignored for pushbutton and radiobutton, in progress Using exit() in batch mode throws octave::exit_exception. fixed Display of images for axes partially outside a figure. fixed uicontrol popupmenu sizing. fixed Implementation of containers.Map. fixed Error in the unwind_protect_cleanup section of print.m.fixed strmatch, incompatible result on 'empty' input, in progress Patch with zero area not displayed with OpenGL, in progress questdlg displays buttons in reverse order. fixed waitfor should silently accept an empty graphics handle. fixed Segmentation fault after a caught error in an Octave script. fixed Non-empty ouput for non-matching regexp with 'names' option. fixed Invalid FID and fopen(FID). fixed Matlab eval function accepts a column vector string input, in progress __have_gnuplot__ does not return anything. fixed uimenu 's position is sometimes 0, in progress rotate3d compatibility with Matlab, in progress Output of uicontrol. fixed isequalwithequalnans is missing. fixed fwrite input argument type. fixed set() is case-sensitive. fixed Update list of missing functions. fixed sum, cumsum, etc. mishandle integer inputs, in progress Error using print and the append flag. fixed ${cmd} replacement operator in regexprep, in progress Position of uimenu. fixed Loading of figures (and other objects) from Octave IDE. fixed orderfields is slow. fixed Undefined input to a classdef method. fixed zeros: like keyword, in progress textscan option MultipleDelimsAsOne does not apply to space or tab characters, in progress ismember fails if the string ends in a space. fixed Infinite loop in normest1. fixed pinv(0) different from Matlab. fixed center() relies on broadcasting. fixed private function in classdef file. fixed max_recursion_depth error in classdef constructor, in progress isequal is slow. fixed display of multidimensional arrays uses 'ans', in progress strcmp with multidimensional char arrays, in progress Implementation of class categorical, in progress Support for "import" keyword, in progress modal windowstyle property not working. fixed Missing keyword help for classdef keywords. fixed makeValidName and makeUniqueStrings. fixed PDF user manual uses a backward apostrophe ` in code examples. fixed Implementation of histcounts, in progress Implement jsondecode, jsonencode functions, in progress Figure property IntegerHandle does not work fully with Qt toolkit, in progress "Number" property for figure. fixed Implementation of movegui. fixed Implementation of savefig. fixed Octave 4.3.0+ can't load figures saved with previous versions, in progress Unknown command `codequoteundirected' in help text. fixed warning message when qcollectiongenerator and qhelpgenerator are not found. fixed Syntax of documentation with texinfo 4.13. fixed Segmentation fault when executing a script containing a figure. fixed warning from opengl_renderer about light object. fixed uicontrol/uibuttongroup: focusing not implemented yet. fixed octave deadlocks with deletefcn callback that calls graphical function, in progress doc: some default Qt properties are different between systems. fixed MEX file in a private directory of a class. fixed ismember error with mixed numeric and char arrays inputs. fixed Error with whos -file: 'load' not found. fixed Behavior of open with unknown or non-existing files, in progress Colors of a uicontrol pushbutton. fixed uipanel doesnt show border in linux. fixed camlight (axis_handle, ...) should work for Matlab Compatibility. fixed Implementation of isfolder. fixed Private directory in +package, in progress Figure's Position when MenuBar is none. fixed load() should issue an error if specified variable does not exist in file, in progress subsasgn call when the subscripted expression contains the end keyword, in progress Implementation of memmapfile, in progress File browser unresponsive, in progress uicontrol: validation of cdata property. fixed savefig should accept a vector of figure handles for Matlab compatibility. fixed colormap property of a figure cannot be empty. fixed Interpreter cannot find methods in files of classdefs in packages, in progress Implement uicontrol focusing behavior. fixed Use of camlight when a patch is not visible. fixed Removal of called_from_builtin, in progress Property VertexNormals not updated. fixed gunzip/bunzip2 error with cell array of strings input. fixed DOCSTRING macro does not recognize matlab.lang.makeValidName. fixed Change of a togglebutton uicontrol's value not reflected graphically. fixed Global variable in a MEX file, in progress warning: popupmenu value not within valid display range. fixed Speed issue with uicontrols, in progress gcbf and HandleVisibility property. fixed Add support for more types for image's cdata. fixed Binary input image for edge, in progress colorbar properties need listeners to invoke actions, in progress Implementation of lightangle. fixed [MXE Octave] lib vs lib64. fixed Path management in the GUI, in progress isosurface is slow. fixed Image not displayed with YDir set to normal. fixed Conflict between package namespace and function name, in progress subsref called in a subscripted assignment operation, in progress statistical CDF functions lack upper argument support, in progress Closing plots much slower in Octave 5.1.0, in progress dbup and dbdown not working as expected, in progress Undecided yet 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. 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). Miscellaneous exist('OCTAVE_VERSION','builtin') can be used to detect if running in Octave or MATLAB.