Dear Volkmar
unfortunately I'm still having trouble!
I tried adding the path then went back into spm5/src and typed "make" but I get the following errors
is it still a path problem? I used bash terminal for the path commands but I think when my matlab was set up it was in /bin/csh/ which is what I type before I type matlab would this have anything to do with the problem?
Thanks in advance
Ciara
/home/cmccabe/spm5/src
cmccabe@psyws11:~/spm5/src> make
_____________________________________________________________
Linux compilation (x86-64) - using gcc
_____________________________________________________________
mex COPTIMFLAGS='-O3 -funroll-loops -fPIC -march=x86-64 -mfpmath=sse' spm_sample_vol.c spm_vol_utils.mexa64.a
spm_sample_vol.o: In function `mexFunction':
spm_sample_vol.c:(.text+0x2c): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0x59): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0x68): undefined reference to `mxIsNumeric'
spm_sample_vol.c:(.text+0x76): undefined reference to `mxIsComplex'
spm_sample_vol.c:(.text+0x98): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0xa7): undefined reference to `mxIsNumeric'
spm_sample_vol.c:(.text+0xb5): undefined reference to `mxIsComplex'
spm_sample_vol.c:(.text+0xd7): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0xea): undefined reference to `mxIsNumeric'
spm_sample_vol.c:(.text+0xf8): undefined reference to `mxIsComplex'
spm_sample_vol.c:(.text+0x11c): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0x124): undefined reference to `mxGetM'
spm_sample_vol.c:(.text+0x12f): undefined reference to `mxGetN'
spm_sample_vol.c:(.text+0x13a): undefined reference to `mxGetM'
spm_sample_vol.c:(.text+0x156): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0x165): undefined reference to `mxIsNumeric'
spm_sample_vol.c:(.text+0x173): undefined reference to `mxIsComplex'
spm_sample_vol.c:(.text+0x195): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0x19e): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x1c8): undefined reference to `mxGetM'
spm_sample_vol.c:(.text+0x1d4): undefined reference to `mxGetN'
spm_sample_vol.c:(.text+0x1eb): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x213): undefined reference to `mxCreateDoubleMatrix_700'
spm_sample_vol.c:(.text+0x228): undefined reference to `mxCreateDoubleMatrix_700'
spm_sample_vol.c:(.text+0x23e): undefined reference to `mxCreateDoubleMatrix_700'
spm_sample_vol.c:(.text+0x253): undefined reference to `mxCreateDoubleMatrix_700'
spm_sample_vol.c:(.text+0x267): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x273): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x27e): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x28e): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x29e): undefined reference to `mxGetPr'
spm_sample_vol.o:spm_sample_vol.c:(.text+0x2ae): more undefined references to `mxGetPr' follow
spm_sample_vol.o: In function `mexFunction':
spm_sample_vol.c:(.text+0x339): undefined reference to `mxCreateDoubleMatrix_700'
spm_sample_vol.c:(.text+0x34c): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x357): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x362): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x371): undefined reference to `mxGetPr'
spm_sample_vol.c:(.text+0x3c6): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0x3d4): undefined reference to `mxGetN'
spm_sample_vol.c:(.text+0x3ee): undefined reference to `mxGetM'
spm_sample_vol.c:(.text+0x403): undefined reference to `mxGetN'
spm_sample_vol.c:(.text+0x44d): undefined reference to `mexErrMsgTxt'
spm_sample_vol.c:(.text+0x45c): undefined reference to `mxIsSparse'
spm_sample_vol.c:(.text+0x46e): undefined reference to `mxIsDouble'
spm_sample_vol.c:(.text+0x480): undefined reference to `mxGetM'
spm_sample_vol.c:(.text+0x48d): undefined reference to `mxGetN'
spm_sample_vol.c:(.text+0x4a5): undefined reference to `mxGetM'
spm_sample_vol.c:(.text+0x4b2): undefined reference to `mxGetN'
spm_sample_vol.c:(.text+0x4d6): undefined reference to `mxIsSparse'
spm_sample_vol.c:(.text+0x4ec): undefined reference to `mxIsDouble'
spm_sample_vol.c:(.text+0x506): undefined reference to `mxIsSparse'
spm_sample_vol.c:(.text+0x51c): undefined reference to `mxIsDouble'
spm_sample_vol.c:(.text+0x536): undefined reference to `mxIsSparse'
spm_sample_vol.c:(.text+0x54c): undefined reference to `mxIsDouble'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `free_maps':
spm_mapping.c:(.text+0xe0): undefined reference to `mxFree'
spm_mapping.c:(.text+0x142): undefined reference to `mxFree'
spm_mapping.c:(.text+0x1a4): undefined reference to `mxFree'
spm_mapping.c:(.text+0x1dc): undefined reference to `mxFree'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `get_map_dat':
spm_mapping.c:(.text+0x20c): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x22f): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x238): undefined reference to `mxIsDouble'
spm_mapping.c:(.text+0x251): undefined reference to `mxIsSingle'
spm_mapping.c:(.text+0x26a): undefined reference to `mxIsInt32'
spm_mapping.c:(.text+0x283): undefined reference to `mxIsUint32'
spm_mapping.c:(.text+0x299): undefined reference to `mxIsInt16'
spm_mapping.c:(.text+0x2af): undefined reference to `mxIsUint16'
spm_mapping.c:(.text+0x2c5): undefined reference to `mxIsInt8'
spm_mapping.c:(.text+0x2db): undefined reference to `mxIsUint8'
spm_mapping.c:(.text+0x300): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x309): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0x316): undefined reference to `mxGetNumberOfDimensions_700'
spm_mapping.c:(.text+0x337): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x340): undefined reference to `mxGetDimensions_700'
spm_mapping.c:(.text+0x3d6): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x3ee): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x3fa): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x41c): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x425): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0x4ea): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x4fd): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x515): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x521): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x534): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x540): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x562): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x56b): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0x5a4): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x649): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x68e): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x6d3): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x752): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x76a): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x779): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x788): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x797): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x7d6): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x7df): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x7ee): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0x81f): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x828): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0x835): undefined reference to `mxGetN'
spm_mapping.c:(.text+0xadb): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0xaf3): undefined reference to `mxGetM'
spm_mapping.c:(.text+0xb02): undefined reference to `mxGetN'
spm_mapping.c:(.text+0xb23): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0xb2c): undefined reference to `mxGetPr'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `get_map_file':
spm_mapping.c:(.text+0xc50): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0xc79): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0xc82): undefined reference to `mxGetM'
spm_mapping.c:(.text+0xc8e): undefined reference to `mxGetN'
spm_mapping.c:(.text+0xcb6): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0xcbf): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0xe07): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0xe58): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0xea9): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0xec6): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0xef2): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0xefb): undefined reference to `mxGetM'
spm_mapping.c:(.text+0xf07): undefined reference to `mxGetN'
spm_mapping.c:(.text+0xf32): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0xf3b): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0x11a9): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x13f9): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1412): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x143e): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1447): undefined reference to `mxIsChar'
spm_mapping.c:(.text+0x1458): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x1464): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x147e): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x1492): undefined reference to `mxGetString_700'
spm_mapping.c:(.text+0x149f): undefined reference to `mxFree'
spm_mapping.c:(.text+0x14c0): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x14e5): undefined reference to `mxFree'
spm_mapping.c:(.text+0x1506): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x152b): undefined reference to `mxFree'
spm_mapping.c:(.text+0x154c): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x162c): undefined reference to `mxFree'
spm_mapping.c:(.text+0x164d): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1656): undefined reference to `mxFree'
spm_mapping.c:(.text+0x166f): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x1687): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x1696): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x16a5): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x16f0): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x16f9): undefined reference to `mxGetPr'
spm_mapping.c:(.text+0x1706): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x17f3): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1b35): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1c28): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1d9b): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x1db3): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x1dc2): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x1de9): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1df2): undefined reference to `mxGetPr'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `get_maps_struct':
spm_mapping.c:(.text+0x1efd): undefined reference to `mxIsStruct'
spm_mapping.c:(.text+0x1f0d): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x1f23): undefined reference to `mxGetNumberOfDimensions_700'
spm_mapping.c:(.text+0x1f2f): undefined reference to `mxGetDimensions_700'
spm_mapping.c:(.text+0x1f83): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x1fa6): undefined reference to `mxGetField_700'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `get_maps_3dvol':
spm_mapping.c:(.text+0x202c): undefined reference to `mxIsDouble'
spm_mapping.c:(.text+0x2045): undefined reference to `mxIsSingle'
spm_mapping.c:(.text+0x205e): undefined reference to `mxIsInt32'
spm_mapping.c:(.text+0x2074): undefined reference to `mxIsUint32'
spm_mapping.c:(.text+0x208a): undefined reference to `mxIsInt16'
spm_mapping.c:(.text+0x20a0): undefined reference to `mxIsUint16'
spm_mapping.c:(.text+0x20b6): undefined reference to `mxIsInt8'
spm_mapping.c:(.text+0x20cc): undefined reference to `mxIsUint8'
spm_mapping.c:(.text+0x20e5): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x20f4): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x2101): undefined reference to `mxGetNumberOfDimensions_700'
spm_mapping.c:(.text+0x2116): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x211f): undefined reference to `mxGetDimensions_700'
spm_mapping.c:(.text+0x21ed): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x220c): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x222b): undefined reference to `mxCalloc'
spm_mapping.c:(.text+0x226e): undefined reference to `mxGetPr'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `get_maps':
spm_mapping.c:(.text+0x2338): undefined reference to `mxIsStruct'
spm_mapping.c:(.text+0x2358): undefined reference to `mxGetNumberOfDimensions_700'
spm_mapping.c:(.text+0x2366): undefined reference to `mxIsNumeric'
spm_mapping.c:(.text+0x2373): undefined reference to `mxIsComplex'
spm_mapping.c:(.text+0x2380): undefined reference to `mxIsSparse'
spm_mapping.c:(.text+0x23a3): undefined reference to `mexErrMsgTxt'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `voxdim':
spm_mapping.c:(.text+0x2463): undefined reference to `sqrt'
spm_vol_utils.mexa64.a(spm_mapping.mexa64.o): In function `get_dtype':
spm_mapping.c:(.text+0x2499): undefined reference to `mxIsStruct'
spm_mapping.c:(.text+0x24a9): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x24c7): undefined reference to `mxGetField_700'
spm_mapping.c:(.text+0x24de): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x24e7): undefined reference to `mxGetM'
spm_mapping.c:(.text+0x24f3): undefined reference to `mxGetN'
spm_mapping.c:(.text+0x2509): undefined reference to `mexErrMsgTxt'
spm_mapping.c:(.text+0x2512): undefined reference to `mxGetPr'
spm_vol_utils.mexa64.a(utils_uchar.mexa64.o): In function `slice_uchar_1':
spm_vol_utils.c:(.text+0x1937): undefined reference to `floor'
spm_vol_utils.c:(.text+0x1981): undefined reference to `floor'
spm_vol_utils.c:(.text+0x19ca): undefined reference to `floor'
spm_vol_utils.mexa64.a(utils_uchar.mexa64.o): In function `slice_uchar_0':
spm_vol_utils.c:(.text+0x1e01): undefined reference to `floor'
spm_vol_utils.c:(.text+0x1e39): undefined reference to `floor'
spm_vol_utils.mexa64.a(utils_uchar.mexa64.o):spm_vol_utils.c:(.text+0x1f46): more undefined references to `floor' follow
spm_vol_utils.mexa64.a(spm_make_lookup.mexa64.o): In function `make_lookup_sinc_grad':
spm_make_lookup.c:(.text+0x1ca4): undefined reference to `sin'
spm_make_lookup.c:(.text+0x1cd1): undefined reference to `cos'
spm_make_lookup.c:(.text+0x1d44): undefined reference to `sin'
spm_make_lookup.c:(.text+0x1d72): undefined reference to `cos'
spm_vol_utils.mexa64.a(spm_make_lookup.mexa64.o): In function `make_lookup_sinc':
spm_make_lookup.c:(.text+0x2006): undefined reference to `floor'
spm_make_lookup.c:(.text+0x204b): undefined reference to `floor'
spm_make_lookup.c:(.text+0x20d6): undefined reference to `floor'
spm_make_lookup.c:(.text+0x2157): undefined reference to `sin'
spm_make_lookup.c:(.text+0x218d): undefined reference to `cos'
spm_make_lookup.c:(.text+0x21f3): undefined reference to `sin'
spm_make_lookup.c:(.text+0x2230): undefined reference to `cos'
spm_make_lookup.c:(.text+0x228a): undefined reference to `sin'
spm_make_lookup.c:(.text+0x22c0): undefined reference to `cos'
spm_make_lookup.c:(.text+0x2309): undefined reference to `sin'
spm_make_lookup.c:(.text+0x2346): undefined reference to `cos'
collect2: ld returned 1 exit status
mex: link of 'spm_sample_vol.mexa64' failed.
make: *** [spm_sample_vol.mexa64] Error 1
cmccabe@psyws11:~/spm5/src>
Dr Ciara McCabe
University of Oxford
Dept of Psychiatry
Neuroscience Building
Warneford Hospital
Oxford
OX3 7JX
Telephone (01865)-223778
mob: 07966035631
[log in to unmask]
http://users.ox.ac.uk/~psyc0288/perl/ciara_mcabe.html
>>> Volkmar Glauche <[log in to unmask]> 12/09/2007 13:23 >>>
dear Ciara,
try to locate your MATLAB folder, there should be a "bin" folder in it
where the mex executable lives. You then need to
- either add the this bin folder to your PATH environment by setting
PATH=$PATH:/path/to/your/matlab/bin
(this is bash syntax)
and then run
make
-or run
MEX=/path/to/your/matlab/bin/mex make
to tell make where your "mex" command resides.
Volkmar
On Wed, 12 Sep 2007, Ciara McCabe wrote:
> Dear Volkmar
>
> as I've got a 64 bit linux with spm5 and matlab7.4 I tired the "make " command and also entered the following "make all suf..etc...".....and got this error to both
>
>
> Linux compilation (x86-64) - using gcc -03 -funroll-loops -fPIC -march=x86-64
> _____________________________________________________________
>
> mex COPTIMFLAGS='-03 -funroll-loops -fPIC -march=x86-64' -c spm_mapping.c
> make: mex: Command not found
> make: *** [spm_mapping.mexa64.o] Error 127
>
> any ideas?
>
> Thanks in advance
> Ciara
>
>
> Dr Ciara McCabe
> University of Oxford
> Dept of Psychiatry
> Neuroscience Building
> Warneford Hospital
> Oxford
> OX3 7JX
> Telephone (01865)-223778
> mob: 07966035631
>
> [log in to unmask]
> http://users.ox.ac.uk/~psyc0288/perl/ciara_mcabe.html
>
>
>
>>>> Volkmar Glauche <[log in to unmask]> 11/09/2007 12:11 >>>
> Dear Ciara,
>
> if you can't display any image, then you probably do not have SPMs mex
> files compiled in a version suitable for MATLAB 7.4. Go to the src
> directory, make sure that the mex command is the one for MATLAB 7.4 and
> type "make". This should recompile and install your mex files.
>
> Volkmar
>
> On Tue, 11 Sep 2007, Ciara McCabe wrote:
>
>> Dear SPMers
>>
>> I am trying to run spm5 with matlab 7.4 but I get the following errors, any ideas on what is going wrong?
>>
>>
>>
>>
>> Initialising SPM.........done
>>
>> SPM present working directory:
>> /home/cmccabe
>>>> --------------------------
>> Running "Display Image"
>> Image "/home/cmccabe/Reward/MRdata/MDS/MDSHR.struct.img" can not be resampled
>> Image "/home/cmccabe/Reward/MRdata/MDS/MDSHR.struct.img" can not be resampled
>>
>> Thanks in advance
>> Ciara
>>
>>
>> Dr Ciara McCabe
>> University of Oxford
>> Dept of Psychiatry
>> Neuroscience Building
>> Warneford Hospital
>> Oxford
>> OX3 7JX
>> Telephone (01865)-223778
>> mob: 07966035631
>>
>> [log in to unmask]
>> http://users.ox.ac.uk/~psyc0288/perl/ciara_mcabe.html
>>
>>
>
>
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg http://fbi.uniklinik-freiburg.de/
|