Sorry. My mistake. SPM2 seems a long time ago now. I was thinking
about SPM5, which has a separate src subdirectory.
Grootjes,
-John
-----Original Message-----
From: Bas Neggers [mailto:[log in to unmask]]
Sent: Friday, June 01, 2007 6:11 PM
To: Ashburner John (PSYCHOLOGY)
Cc: [log in to unmask]; Yi Sun
Subject: Re: [SPM] Error when using SPM2
... 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
--------------------------------------------------
|