FieldTrip

The fieldtrip version on the ftp server includes compile mex files for the most common platforms. Hoever, it might be that you have a platform (OS and Matlab combination) on which the precompiled mex files are not included, and then you'll have to compile them yourself.

The source code for the mex files is included with the fieldtrip release, at the same place as where the mex files are supposed to be located. Since most of the mex files are low-level functions, you will mainly find them in the “private” directories. You can recompile the mex files for your platform using the following commands:

cd ../somehere/private
mex meg_leadfield1.c
mex plgndr.c
mex read_24bit.c

The following files all depend on some shared code in geometry.c and geometry.h, hence the compilation process is slighty different for these:

mex -I. -c geometry.c		
mex -I. -c solid_angle.c ; mex -o solid_angle solid_angle.o geometry.o
mex -I. -c lmoutr.c      ; mex -o lmoutr      lmoutr.o      geometry.o
mex -I. -c ptriproj.c    ; mex -o ptriproj    ptriproj.o    geometry.o
mex -I. -c ltrisect.c    ; mex -o ltrisect    ltrisect.o    geometry.o
mex -I. -c routlm.c      ; mex -o routlm      routlm.o      geometry.o
mex -I. -c plinproj.c    ; mex -o plinproj    plinproj.o    geometry.o

If you are on a Windows computer, the compiled object files with have extension *.obj instead of *.o and hence you then should do

mex -I. -c geometry.c
mex -I. -c solid_angle.c ; mex solid_angle.c solid_angle.obj geometry.obj
mex -I. -c lmoutr.c      ; mex lmoutr.c      lmoutr.obj      geometry.obj
mex -I. -c ptriproj.c    ; mex ptriproj.c    ptriproj.obj    geometry.obj
mex -I. -c ltrisect.c    ; mex ltrisect.c    ltrisect.obj    geometry.obj
mex -I. -c routlm.c      ; mex routlm.c      routlm.obj      geometry.obj
mex -I. -c plinproj.c    ; mex plinproj.c    plinproj.obj    geometry.obj

After compilation the mex files are automatically at the right location.

Note that most of the mex files include a m-file wrapper which will try to do an auto compilation. Again, the autocompilation has not (and can not) be tested on all possible platforms, so your mileage may vary.

If you are using the Visual Studio Compiler and get an error similar to:

error LNK2005: mexFunction already defined in ptriproj.obj

then try this line replacing ptriproj with the file you are trying to compile.

mex -I. -c ptriproj.c    ; mex ptriproj.c  geometry.obj

Note in Linux: If you are get the error message “cannot find -lstdc++”, you can install the libstdc++5 package using your package manager. If, after the install of libtdc++5, the lstdc++ error persists, just do a symbolic link like

ln -s /usr/lib64/libstdc++.so.6 /usr/lib64/libstdc++.so 

and it should work.