Hi,

I have been trying to set up nifty_rec to work with MATLAB, but so far unsuccessfully.

1) After installing the binaries I tried to run some of the demos (I am running Windows 7 64-bit but I have 32-bit MATLAB) but I get the following error:
------------------------------------------------------------------------------------------------------
>> tt_demo_mlem_parallel
Invalid MEX-file 'C:\Program Files (x86)\NiftyRec\niftyrec\matlab\et_rotate_mex.mexw32': The application has failed to start because its side-by-side configuration is incorrect.
Please see the application event log or use the command-line sxstrace.exe tool for more detail.

Error in et_rotate (line 58)
out_image = et_rotate_mex(in_image, rotation, center, use_gpu, background);

Error in tt_demo_mlem_parallel (line 27)
phantom_attenuation = mask.*et_rotate(attenuation_128,[pi/2,0,0],[64.5,64.5,64.5],1,0)*1e-5;
------------------------------------------------------------------------------------------------------
Looking in the event log and around the Internet it seems that this is related to MS Visual C++ Redistributable packages that may or may not be correctly referenced. I have uninstalled and re-installed all MSVC++ Redistributable (2005, 2008, 2010, including service packs) but the problem persists.

Has anyone else experienced this problem or have any other ideas?

2) In a parallel attempt to get things working, I have also tried to build the binaries myself using Cmake and Visual Studio. I am assuming that in this case I should build the mexw32 files from within MATLAB. However when I try to run mex, I get the following error:

>> mex -v _et_rotate_mex.cpp
***************************************************************************
Warning: Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require
the use of -largeArrayDims and remove the -compatibleArrayDims
option. For more information, see:

http://www.mathworks.com/help/techdoc/matlab_external/bsflnue-1.html

****************************************************************************

-> Default options filename found in C:\Users\nly17915\AppData\Roaming\MathWorks\MATLAB\R2012b
----------------------------------------------------------------
-> Options file = C:\Users\nly17915\AppData\Roaming\MathWorks\MATLAB\R2012b\mexopts.bat
MATLAB = C:\Program Files (x86)\MATLAB\R2012b
-> COMPILER = lcc
-> Compiler flags:
COMPFLAGS = -c -I"C:\Program Files (x86)\MATLAB\R2012b\sys\lcc\include" -DMATLAB_MEX_FILE -noregistrylookup
OPTIMFLAGS = -DNDEBUG
DEBUGFLAGS = -g4
arguments =
Name switch = -Fo
-> Pre-linking commands =
-> LINKER = lcclnk
-> Link directives:
LINKFLAGS = -tmpdir "." -dll "C:\Program Files (x86)\MATLAB\R2012b\extern\lib\win32\lcc\mexFunction.def" -L"C:\Program Files (x86)\MATLAB\R2012b\sys\lcc\lib" -libpath "C:\Program Files (x86)\MATLAB\R2012b\extern\lib\win32\lcc" "C:\Users\nly17915\AppData\Local\Temp\mex_R9lSua\templib2.obj"
LINKDEBUGFLAGS =
LINKFLAGSPOST = libmx.lib libmex.lib libmat.lib
Name directive = -o "_et_rotate_mex.mexw32"
File link directive =
Lib. link directive =
Rsp file indicator = @
-> Resource Compiler = lrc -I"C:\Program Files (x86)\MATLAB\R2012b\sys\lcc\include" -noregistrylookup -fo"mexversion.res"
-> Resource Linker =
----------------------------------------------------------------

--> lcc -c -I"C:\Program Files (x86)\MATLAB\R2012b\sys\lcc\include" -DMATLAB_MEX_FILE -noregistrylookup -FoC:\Users\nly17915\AppData\Local\Temp\mex_R9lSua\_et_rotate_mex.obj -I"C:\Program Files (x86)\MATLAB\R2012b\extern\include" -I"C:\Program Files (x86)\MATLAB\R2012b\simulink\include" -DNDEBUG -DMX_COMPAT_32 _et_rotate_mex.cpp

lcc preprocessor error: _et_rotate_mex.cpp:12 Could not find include file "_et_array_interface.h"
lcc preprocessor error: _et_rotate_mex.cpp:14 Could not find include file <limits>
lcc preprocessor error: _et_rotate_mex.cpp:17 Could not find include file <cmath>
Error _et_rotate_mex.cpp: 29 illegal statement termination
Error _et_rotate_mex.cpp: 29 skipping `const'
Error _et_rotate_mex.cpp: 29 illegal use of type name `mxClassID'
Warning _et_rotate_mex.cpp: 29 Statement has no effect
Error _et_rotate_mex.cpp: 29 syntax error; found `cid_image' expecting `;'
Error _et_rotate_mex.cpp: 29 undeclared identifier `cid_image'
Error _et_rotate_mex.cpp: 30 illegal statement termination
Error _et_rotate_mex.cpp: 30 skipping `const' `int'
Error _et_rotate_mex.cpp: 30 undeclared identifier `dim_image'
Error _et_rotate_mex.cpp: 32 illegal statement termination
Error _et_rotate_mex.cpp: 32 skipping `const'
Error _et_rotate_mex.cpp: 32 illegal use of type name `mxClassID'
Warning _et_rotate_mex.cpp: 32 Statement has no effect
Error _et_rotate_mex.cpp: 32 syntax error; found `cid_rotation' expecting `;'
Error _et_rotate_mex.cpp: 32 undeclared identifier `cid_rotation'
Error _et_rotate_mex.cpp: 33 illegal statement termination
Error _et_rotate_mex.cpp: 33 skipping `const' `int'
Error _et_rotate_mex.cpp: 33 undeclared identifier `dim_rotation'
Error _et_rotate_mex.cpp: 35 illegal statement termination
Error _et_rotate_mex.cpp: 35 too many errors

C:\PROGRA~2\MATLAB\R2012B\BIN\MEX.PL: Error: Compile of '_et_rotate_mex.cpp' failed.

Error using mex (line 206)
Unable to complete successfully.

---------------------------------------------------------------- ----------------------------------------------------------------

It seems that it cannot find some header files, although I have added the entire nifty_rec directory to the path. In fact, I can just open the file _et_array_interface.h in the MATLAB editor, yet somehow mex doesn't see it...

Any help will be much appreciated.

Chrysi

Hi Stefano,

Thanks for your reply!
I had indeed tried building the binaries. After some puzzling, I have now figured out that some cmake variables needed to be set that were not described in the wiki (there is a broken link to a screenshot, maybe this is where the info should be?). I will list them here for others who might run into similar issues:
MATLAB_ENG_LIBRARY: <matlabroot>/extern/lib/win32/microsoft/libeng.lib [the exact path depends on the installed compilers, I have MS visual studio so ]
MATLAB_INCLUDE: <matlabroot>/extern/include
MATLAB_LIBS_DIR: <matlabroot>/BIN/WIN32
MATLAB_MEX_LIBRARY <matlabroot>/extern/lib/win32/microsoft/libmex.lib
MATLAB_MX_LIBRARY <matlabroot>/extern/lib/win32/microsoft/libmx.lib
I also attach a screenshot of all my settings, which worked.

[This: http://b-tk.googlecode.com/svn-history/r10/BTK/branches/SOFAMEA/CMake/FindMatlab.cmake
is where I found which values the cmake variable should have.]

Then I build the project in MSVC 2010 where everything works fine, no errors.

Then I go to MATLAB, add the paths to the build files, the data directory and the m files to the MATLAB path and try to run tt_demo_mlem_parallel. So m files, mex files and data are all visible to MATLAB.

At this point MATLAB crashes with a segmentation fault, see .txt file for details.

Any ideas?

Thanks for your time,
Chrysi

Hi Stefano,
With the other 2 demo files you mention, MATLAB doesn't crash but produces the following errors:
>> et_demo_mlem
Creating synthetic sinogram..
Visualising sinogram..
Undefined function or variable 'N_projections'.

Error in et_demo_mlem (line 59)
for i=1:N_projections

et_list_gpus()
Error using et_list_gpus_mex
Error while querying GPU info.

Error in et_list_gpus (line 26)
gpus = et_list_gpus_mex();

I tried to figure out what happens during the crash of tt_demo_mlem_parallel by examining the log file, no luck so far but I will keep looking.

Chrysi

Also maybe relevant, the error message for tt_demo_mlem_conebeam

>> tt_demo_mlem_conebeam
Mex file entry point is missing. Please check the (case-sensitive)
spelling of mexFunction (for C MEX-files), or the (case-insensitive)
spelling of MEXFUNCTION (for FORTRAN MEX-files).
Invalid MEX-file 'C:\Windows\system32\version.dll': The specified module could not be found.

Error in load_nii_hdr>header_key (line 183)
v6 = version;

Error in load_nii_hdr>read_header (line 148)
dsr.hk = header_key(fid);

Error in load_nii_hdr (line 92)
hdr = read_header(fid);

Error in load_nii (line 122)
[nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);

Error in et_load_nifti (line 13)
[nifti_struct]= load_nii(filename);

Error in tt_demo_mlem_conebeam (line 35)
attenuation = et_load_nifti('attenuation_02_128.nii');

Hi Chrysi,

There seems to be a problem reading the Nifti file (.nii).
It is difficult to say what causes the problem as I have no means to reproduce it.
You can try loading the file with e.g. http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
or to use another phantom, not necessarily from a .nii file.

tt_demo_mlem_conebeam currently has only the GPU implementation, while tt_demo_mlem_parallel has the CPU or GPU option.
So if there is no GPU installed, that might be the reason of the crash.

Stefano