I've reinstalled spm8.zip package and afterwards
this is what I get when running the following command
>make && make install
_____________________________________________________________
Linux compilation (x86-64)
_____________________________________________________________
mex -O -c spm_vol_utils.c -DSPM_UNSIGNED_CHAR
make: mex: Command not found
make: *** [utils_uchar.mexa64.o] Error 12
Iwo
>-----Original Message-----
>From: Guillaume Flandin [mailto:[log in to unmask]]
>Sent: 05 September 2014 13:00
>To: Iwo Bohr
>Cc: [log in to unmask]
>Subject: Re: [SPM] DARTEL for GLNX64
>
>Dear Iwo,
>
>then you definitely have missing files in your SPM8 installation as the
>spm8.zip archive does contain spm8/toolbox/DARTEL/optimNn.mexa64
>(which
>hasn't changed since 2008).
>I'd suggest you reinstall SPM8:
> https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#SPM8
>You actually do not need to install the updates as they are already
>included in the spm8.zip archive you can download from our website. It
>also already contains compiled MEX files for Linux, Mac and Windows, 32
>and 64 bit.
>
>Best regards,
>Guillaume.
>
>
>On 05/09/14 12:41, Iwo Bohr wrote:
>> Dear Guillaume,
>>
>> Here it is:
>>
>> Iwo@NMRC51:/mnt/Iwo/mriarchive/VBM$> ls
>/home/login/spm8/toolbox/DARTEL/optimNn.*
>> /home/login/spm8/toolbox/DARTEL/optimNn.m
>> /home/login/spm8/toolbox/DARTEL/optimNn.mexmaci
>> /home/login/spm8/toolbox/DARTEL/optimNn.mexw32
>> /home/login/spm8/toolbox/DARTEL/optimNn.mexglx
>> /home/login/spm8/toolbox/DARTEL/optimNn.mexmaci64
>> /home/login/spm8/toolbox/DARTEL/optimNn.mexw64
>>
>> Iwo
>>
>>> -----Original Message-----
>>> From: Guillaume Flandin [mailto:[log in to unmask]]
>>> Sent: 05 September 2014 12:20
>>> To: Iwo Bohr
>>> Cc: [log in to unmask]
>>> Subject: Re: [SPM] DARTEL for GLNX64
>>>
>>> Dear Iwo,
>>>
>>> the error you get is due to a change in MATLAB's setxor that took place
>>> after the release of SPM8 you are using. A quick fix is to change
>>> spm_check_installation.m line 380 so that it reads:
>>> if isempty(ir) && isempty(il)
>>> It should hopefully run successfully afterwards. Otherwise, what we
>>> really want to see is the output of:
>>> ls /home/login/spm8/toolbox/DARTEL/optimNn.*
>>>
>>> Best regards,
>>> Guillaume.
>>>
>>>
>>> On 05/09/14 10:42, Iwo Bohr wrote:
>>>> Hello John and Guillome,
>>>>
>>>>
>>>>
>>>> This is the what the script 'spm_check_installation full' returned in my
>>>> case (incl. some errors):
>>>>
>>>>
>>>>
>>>> SPM is installed in: /home/login/spm8
>>>>
>>>> SPM version is SPM8 (5236, 04 Feb 13)
>>>>
>>>> SPM toolboxes: none
>>>>
>>>> MATLAB is installed in: /usr/local/MATLAB/R2013b
>>>>
>>>> MATLAB version is 8.2.0.701 (R2013b)
>>>>
>>>> MATLAB toolboxes: signal (v6.20) images (v8.3) stats (v8.3)
>>>>
>>>> Platform: GLNXA64 (maxsize=281474976710655)
>>>>
>>>> OS: Linux 3.9.10-100.fc17.x86_64 #1 SMP Sun Jul 14 01:31:27 UTC 2013
>>> x86_64
>>>>
>>>> Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server
>>>> VM mixed mode
>>>>
>>>> Java support: jvm awt swing
>>>>
>>>> Monitor(s): [0 0 1434 810] (24bit)
>>>>
>>>> OpenGL version: 1.2 (1.5 Mesa 6.4.1)(Hardware)
>>>>
>>>> OpenGL renderer: Mesa project: www.mesa3d.org (Mesa GLX Indirect)
>>>>
>>>> MEX extension: mexa64
>>>>
>>>> C Compiler: GNU C ().
>>>>
>>>> C Compiler settings: gcc ('-O -DNDEBUG')
>>>>
>>>> C Source code permissions: dir rwxr-xr-x, file rw-r--r--
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Directory : /home/login/spm8
>>>>
>>>> SVN Id does not match filename for file:
>>>>
>>>> /home/login/spm8/Zspm_defaults.m
>>>>
>>>> Directory : /home/login/spm8/external/fieldtrip/private
>>>>
>>>> SVN Id does not match filename for file:
>>>>
>>>> /home/login/spm8/external/fieldtrip/private/volumeedit.m
>>>>
>>>> Parsing local installation... ...done
>>>>
>>>> Downloading SPM information... ...done
>>>>
>>>> Parsing SPM information... ...done
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Error using horzcat
>>>>
>>>> Dimensions of matrices being concatenated are not consistent.
>>>>
>>>>
>>>>
>>>> Error in spm_check_installation>compare_versions (line 380)
>>>>
>>>> if isempty([ir il])
>>>>
>>>>
>>>>
>>>> Error in spm_check_installation>check_full (line 364)
>>>>
>>>> compare_versions(l,r);
>>>>
>>>>
>>>>
>>>> Error in spm_check_installation (line 27)
>>>>
>>>> check_full;
>>>>
>>>>
>>>>
>>>> *From:*John Ashburner [mailto:[log in to unmask]]
>>>> *Sent:* 04 September 2014 18:30
>>>> *To:* Iwo Bohr
>>>> *Cc:* [log in to unmask]
>>>> *Subject:* Re: [SPM] DARTEL for GLNX64
>>>>
>>>>
>>>>
>>>> Is it possible that there is some form of installation problem.
>>>> Guillaume suggests to me that you could try the following to make sure
>>>> all the files have been extracted to the right place:
>>>>
>>>>
>>>>
>>>> spm_check_installation full
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On my SPM8 version (and in the official release) I see the following:
>>>>
>>>>
>>>>
>>>> john@ash:~/Documents/spm8$ ls toolbox/DARTEL/optimNn.*
>>>>
>>>> toolbox/DARTEL/optimNn.m toolbox/DARTEL/optimNn.mexmaci64
>>>>
>>>> toolbox/DARTEL/optimNn.mexa64 toolbox/DARTEL/optimNn.mexw32
>>>>
>>>> toolbox/DARTEL/optimNn.mexglx toolbox/DARTEL/optimNn.mexw64
>>>>
>>>> toolbox/DARTEL/optimNn.mexmaci
>>>>
>>>>
>>>>
>>>> Perhaps your version is missing one or more of these files.
>>>>
>>>> Best regards,
>>>>
>>>> -John
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 4 September 2014 18:01, Iwo Bohr <[log in to unmask]
>>>> <mailto:[log in to unmask]>> wrote:
>>>>
>>>> It's SPM8 .
>>>>
>>>> I can't remember the exact error messages (should have noted it down, I
>>>> know L) but it was something about uncompelled files...
>>>>
>>>> Well it's easy to reproduce it for New Segment , because it happens at
>>>> the very beginning of running it:
>>>>
>>>>
>>>>
>>>> "Running 'New Segment'
>>>>
>>>> Failed 'New Segment'
>>>>
>>>> Error using optimNn (line 68)
>>>>
>>>> Not compiled for GLNXA64 in MATLAB 8.2.0.701 (R2013b) (see make.m)
>>>>
>>>>
>>>>
>>>> In file "/home/login/spm8/toolbox/DARTEL/optimNn.m" (v1143),
>function
>>>> "optimNn" at line 68.
>>>>
>>>> In file "/home/login/spm8/toolbox/Seg/spm_preproc8.m" (v4148),
>function
>>>> "spm_preproc8" at line 818.
>>>>
>>>> In file "/home/login/spm8/toolbox/Seg/spm_preproc_run.m" (v4677),
>>>> function "run_job" at line 106.
>>>>
>>>> In file "/home/login/spm8/toolbox/Seg/spm_preproc_run.m" (v4677),
>>>> function "spm_preproc_run" at line 30.
>>>>
>>>> In file "/home/login/spm8/toolbox/Seg/tbx_cfg_preproc8.m" (v4337),
>>>> function "spm_local_preproc_run" at line 363."
>>>>
>>>>
>>>>
>>>> It was something similar while trying to run the batch with old Segment,
>>>> but occurring at "run Dartel" component.
>>>>
>>>>
>>>>
>>>> Iwo
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *From:*John Ashburner [mailto:[log in to unmask]
>>>> <mailto:[log in to unmask]>]
>>>> *Sent:* 04 September 2014 17:48
>>>> *To:* Iwo Bohr
>>>> *Cc:* [log in to unmask] <mailto:[log in to unmask]>
>>>> *Subject:* Re: [SPM] DARTEL for GLNX64
>>>>
>>>>
>>>>
>>>> Which version of SPM are you using? Older versions were developed
>>>> before 64 bit systems were widely available. Also, what error messages
>>>> were produced? These usually give some sort of clue about what's gone
>>>> wrong.
>>>>
>>>>
>>>>
>>>> Best regards,
>>>>
>>>> -John
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 4 September 2014 17:06, Iwo Bohr <[log in to unmask]
>>>> <mailto:[log in to unmask]>> wrote:
>>>>
>>>> Dear SPM developers,
>>>>
>>>> I've tried twice to run DARTEL batch (Seg+Dartel+MNI reg) on Linux64
>>>> and twice I encountered an unpleasant surprise after a significant time
>>>> of running it:
>>>> using consecutively Old or New Segment as initial steps.
>>>> In both cases it was due to the fact that some routines along the way
>>>> weren't compiled for 64-bit system.
>>>> For the Old Seg version it was more painful because the error occurred
>>>> after two initial steps (seg+import) when everything was seemingly ok.
>>>>
>>>> Would it be possible to give an indication for the updates for these
>>>> "troublesome" routines? Apparently according to the output of
>>> spm_update
>>>> my download is ok.
>>>> Also I think it would be helpful if some sanity check for the system
>>>> would be introduced for out of date routines, it would save a lot of
>>>> time spent on trying running out of date procedures. After all I
>>>> downloaded my SPM not that long time ago (about 1 yr) when 32bit
>systems
>>>> were already commonly in use...
>>>>
>>>> Many thanks,
>>>> Iwo
>>>>
>>>> ---
>>>> Iwo Bohr, PhD
>>>> Research Associate,
>>>> Newcastle Magnetic Resonance Centre
>>>> Campus for Ageing and Vitality,
>>>> Newcastle University,
>>>> Newcastle upon Tyne, NE4 5PL, UK
>>>> Tel. +44 191 208 1160 <tel:%2B44%20191%20208%201160>
>>>> Webpage: http://www.ncl.ac.uk/magres/staff/profile/iwo.bohr
>>>> http://scholar.google.co.uk/citations?user=-0AKmt4AAAAJ
>>>>
>>>>
>>>> http://www.charliecroweappeal.com/
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> Guillaume Flandin, PhD
>>> Wellcome Trust Centre for Neuroimaging
>>> University College London
>>> 12 Queen Square
>>> London WC1N 3BG
>
>--
>Guillaume Flandin, PhD
>Wellcome Trust Centre for Neuroimaging
>University College London
>12 Queen Square
>London WC1N 3BG
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