Hello Bas and John,
I did some tests on my computer and the problem was solved.
The system and softwares I used were:
Fedora 6 (32 bits), Matlab 2006b and SPM2.
I disabled selinux, at this moment, the SPM2 can work. But Because the selinux
is disabled, I am not sure if this may cause any other problems later...
Thanks for your tips!
Yi
Quoting Bas Neggers <[log in to unmask]>:
> ... my spm2 source tree never had a src folder, *.c files and
> Makefile were right in spm2 ...
>
> Kind regards to Maastricht,
>
> Bas
>
>
> Ashburner John (PSYCHOLOGY) schreef:
>> Maybe the newly compiled files need to be moved from spm/src into the
>> spm directory??
>>
>> Best regards,
>> -John
>>
>> -----Original Message-----
>> From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
>> On Behalf Of Neggers, S.F.W.
>> Sent: Friday, June 01, 2007 5:45 PM
>> To: [log in to unmask]
>> Subject: Re: [SPM] Error when using SPM2
>>
>> Dear Yi, list,
>>
>> looks like your compilation comleted all right, so that is not the
>> issue. I'd also contact your system administrator as this might be a
>> local issue on your system.
>>
>> I am not very familiar with the mex binaries en accompanying errors, but
>> perhaps you have a 'rights' problem with these files? Just a hunch
>> because I read something like 'permission denied'...
>>
>> Do you have a 64 bit processor? You might have to tweak your spm2
>> Makefile to have it work for 64 bit systems. I noticed that spm5
>> supports 64 bit very well out of the box, unlike spm2 (which makes
>> sense, 64 bit was not common back then).
>>
>> You might want to do a search on the JISCMAIL archive, during my
>> previous job I once posted an spm2 Makefile for 64 bit on the mail list.
>> I do not have access to that machine at my previous lab right now... I
>> remember others posted Makefiles as well.
>>
>> Cheers,
>>
>> Bas
>>
>> --------------------------------------------------
>> Dr. S.F.W. Neggers
>> Division of Brain Research
>> Rudolf Magnus Institute for Neuroscience
>> Utrecht University Medical Center
>>
>> Visiting : Heidelberglaan 100, 3584 CX Utrecht
>> Room A.00.1.24
>> Mail : Huispost A.01.126, P.O. Box
>> 3508 GA Utrecht, the Netherlands
>> Tel : +31 (0)30 2503386 Fax : +31 (0)30 2505443
>> E-mail : [log in to unmask] Web :
>> http://www.fmri.nl/people/bas.html
>> --------------------------------------------------
>>
>>
>>
>> -----Oorspronkelijk bericht-----
>> Van: SPM (Statistical Parametric Mapping) namens Yi Sun
>> Verzonden: vr 1-6-2007 16:13
>> Aan: [log in to unmask]
>> Onderwerp: [SPM] Error when using SPM2
>> Hello Bas,
>>
>> I tried to "make" the file. and I got the following results:
>>
>> make[1]: Entering directory `/home/Yi/spm2'
>> make all SUF=mexglx CC="gcc -O3 -funroll-loops" MEX="mex
>> COPTIMFLAGS='-O3
>> -funroll-loops'"
>> make[2]: Entering directory `/home/Yi/spm2'
>> _____________________________________________________________
>>
>> Linux compilation (Matlab 6.x) - using gcc
>> _____________________________________________________________
>>
>> gcc -O3 -funroll-loops -c -o utils_uchar.mexglx.o spm_vol_utils.c
>> -DSPM_UNSIGNED_CHAR
>> gcc -O3 -funroll-loops -c -o utils_short.mexglx.o spm_vol_utils.c
>> -DSPM_SIGNED_SHORT
>> gcc -O3 -funroll-loops -c -o utils_int.mexglx.o spm_vol_utils.c
>> -DSPM_SIGNED_INT
>> gcc -O3 -funroll-loops -c -o utils_schar.mexglx.o spm_vol_utils.c
>> -DSPM_SIGNED_CHAR
>> gcc -O3 -funroll-loops -c -o utils_ushort.mexglx.o spm_vol_utils.c
>> -DSPM_UNSIGNED_SHORT
>> gcc -O3 -funroll-loops -c -o utils_uint.mexglx.o spm_vol_utils.c
>> -DSPM_UNSIGNED_INT
>> gcc -O3 -funroll-loops -c -o utils_float.mexglx.o spm_vol_utils.c
>> -DSPM_FLOAT
>> gcc -O3 -funroll-loops -c -o utils_double.mexglx.o spm_vol_utils.c
>> -DSPM_DOUBLE
>> gcc -O3 -funroll-loops -c -o utils_short_s.mexglx.o spm_vol_utils.c
>> -DSPM_SIGNED_SHORT -DSPM_BYTESWAP
>> gcc -O3 -funroll-loops -c -o utils_int_s.mexglx.o spm_vol_utils.c
>> -DSPM_SIGNED_INT -DSPM_BYTESWAP
>> gcc -O3 -funroll-loops -c -o utils_ushort_s.mexglx.o spm_vol_utils.c
>> -DSPM_UNSIGNED_SHORT -DSPM_BYTESWAP
>> gcc -O3 -funroll-loops -c -o utils_uint_s.mexglx.o spm_vol_utils.c
>> -DSPM_UNSIGNED_INT -DSPM_BYTESWAP
>> gcc -O3 -funroll-loops -c -o utils_float_s.mexglx.o spm_vol_utils.c
>> -DSPM_FLOAT
>> -DSPM_BYTESWAP
>> gcc -O3 -funroll-loops -c -o utils_double_s.mexglx.o spm_vol_utils.c
>> -DSPM_DOUBLE -DSPM_BYTESWAP
>> gcc -O3 -funroll-loops -c -o spm_make_lookup.mexglx.o spm_make_lookup.c
>> gcc -O3 -funroll-loops -c -o spm_getdata.mexglx.o spm_getdata.c
>> gcc -O3 -funroll-loops -c -o spm_vol_access.mexglx.o spm_vol_access.c
>> mex COPTIMFLAGS='-O3 -funroll-loops' -c spm_mapping.c
>> mv spm_mapping.o spm_mapping.mexglx.o
>> rm -f spm_vol_utils.mexglx.a
>> ar rcv spm_vol_utils.mexglx.a utils_uchar.mexglx.o utils_short.mexglx.o
>> utils_int.mexglx.o utils_schar.mexglx.o utils_ushort.mexglx.o
>> utils_uint.mexglx.o utils_float.mexglx.o utils_double.mexglx.o
>> utils_short_s.mexglx.o utils_int_s.mexglx.o utils_ushort_s.mexglx.o
>> utils_uint_s.mexglx.o utils_float_s.mexglx.o utils_double_s.mexglx.o
>> spm_make_lookup.mexglx.o spm_getdata.mexglx.o spm_vol_access.mexglx.o
>> spm_mapping.mexglx.o
>> a - utils_uchar.mexglx.o
>> a - utils_short.mexglx.o
>> a - utils_int.mexglx.o
>> a - utils_schar.mexglx.o
>> a - utils_ushort.mexglx.o
>> a - utils_uint.mexglx.o
>> a - utils_float.mexglx.o
>> a - utils_double.mexglx.o
>> a - utils_short_s.mexglx.o
>> a - utils_int_s.mexglx.o
>> a - utils_ushort_s.mexglx.o
>> a - utils_uint_s.mexglx.o
>> a - utils_float_s.mexglx.o
>> a - utils_double_s.mexglx.o
>> a - spm_make_lookup.mexglx.o
>> a - spm_getdata.mexglx.o
>> a - spm_vol_access.mexglx.o
>> a - spm_mapping.mexglx.o
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_sample_vol.c
>> spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_slice_vol.c
>> spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_brainwarp.c
>> spm_vol_utils.mexglx.a
>> spm_matfuns.c
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_add.c spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_conv_vol.c
>> spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_render_vol.c
>> spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_global.c spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_resels_vol.c
>> spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_bsplinc.c
>> spm_vol_utils.mexglx.a
>> mex COPTIMFLAGS='-O3 -funroll-loops' spm_bias_mex.c
>> spm_vol_utils.mexglx.a
>> _____________________________________________________________
>>
>> FINISHED
>> _____________________________________________________________
>>
>> make[2]: Leaving directory `/home/Yi/spm2'
>> make[1]: Leaving directory `/home/Yi/spm2'
>>
>> and then I tried again.. I type directly in MATLAB "spm_slice_vol" I
>> got the
>> same error message:
>> ??? Invalid MEX-file '/home/Yi/spm2/spm_slice_vol.mexglx':
>> /home/Yi/spm2/spm_slice_vol.mexglx: cannot restore segment prot after
>> reloc:
>> Permission denied.
>>
>> could you please give me some more detailed information. should I need
>> to adjust
>> the spm_plateform.m file? how should I do this?
>> Thanks again!
>>
>> Yi
>>
>
>
> --
> --------------------------------------------------
> Dr. S.F.W. Neggers
> Division of Brain Research
> Rudolf Magnus Institute for Neuroscience
> Utrecht University Medical Center
>
> Visiting : Heidelberglaan 100, 3584 CX Utrecht
> Room B.01.1.03
> Mail : Huispost B.01.206, P.O. Box 85500
> 3508 GA Utrecht, the Netherlands
> Tel : +31 (0)30 2503386
> Fax : +31 (0)30 2505443
> E-mail : [log in to unmask]
> Web : http://www.fmri.nl/people/bas.html
> --------------------------------------------------
>
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