... I have a feeling you two can help eachother out ....
have fun,
Bas
Yi Sun schreef:
> 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
>> --------------------------------------------------
--
--------------------------------------------------
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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