Dear Jordi,
this is not yet implemented. You can use the standalone version only via the GUI, but it's not yet possible to all it as batch.
Best,
Christian
On Tue, 3 Sep 2019 17:59:41 +0200, Jordi Huguet <[log in to unmask]> wrote:
>Dear Christian et al.,
>
>Are there any any news regarding this topic so far? Would it be possible to
>run CAT12 without depending on a Matlab proprietary license (i.e. using MCR
>+ standalone SPM12)?
>
>My attempts at manually running a CAT12 job via (standalone) SPM12 user
>interface did not succeed, see below:
>
>:~/scratch/cat12/20190801> /opt/packages/spm/12-r7487/run_spm12.sh
>> /opt/packages/mcr/v95 fmri
>> ------------------------------------------
>> Setting up environment variables
>> ---
>> LD_LIBRARY_PATH is
>> .:/opt/packages/mcr/v95/runtime/glnxa64:/opt/packages/mcr/v95/bin/glnxa64:/opt/packages/mcr/v95/sys/os/glnxa64:/opt/packages/mcr/v95/sys/opengl/lib/glnxa64
>> ___ ____ __ __
>> / __)( _ \( \/ )
>> \__ \ )___/ ) ( Statistical Parametric Mapping
>> (___/(__) (_/\/\_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/
>>
>> SPM12: v7487 17:42:24 - 03/09/2019
>> ========================================================================
>> Initialising SPM : ........done
>> SPM present working directory:
>> /home/jhuguet/scratch/cat12/20190801
>> ~ - SPM12: cat12 toolbox ------------------------------------------
>> Toolbox directory prepended to MATLAB path:
>> /data/packages/spm/12-r7487/spm12_mcr/spm12/spm12/toolbox/cat12
>> ----------------------------------------- 17:42:59 - 03/09/2019
>> Error using evalin
>> Undefined function or variable 'cat12'.
>
>
>
>Error in spm (line 946)
>
>
>
>Error using waitforallfiguresclosed (line 9)
>> Error while evaluating UIControl Callback.
>
>
>
>Bye for now...
>
>
>Any help would be greatly appreciated.
>
>Many thanks,
>Jordi
>
>On Mon, Jun 17, 2019 at 12:45 PM Christian Gaser <
>[log in to unmask]> wrote:
>
>> Dear Jordi,
>>
>> I hope that it will be finished in the next 2-3 weeks.
>>
>> Best,
>>
>> Christian
>>
>> On 17 Jun 2019, at 11:47, Jordi Huguet wrote:
>>
>> > Dear Christian,
>> >
>> > I see, what a pity. Do you have an approximate date or time-frame for
>> > the
>> > release of such new version?
>> >
>> > Many thanks,
>> > Jordi
>> >
>> > On Mon, Jun 17, 2019 at 8:35 AM Christian Gaser
>> > <[log in to unmask]>
>> > wrote:
>> >
>> >> Dear Jordi,
>> >>
>> >> the use of the batch shell scripts is not yet supported in the
>> >> deployed
>> >> (compiled) version of CAT12.m This will be added in the next release.
>> >>
>> >> Best,
>> >>
>> >> Christian
>> >>
>> >> On Sat, 15 Jun 2019 17:02:30 +0200, Jordi Huguet <[log in to unmask]>
>> >> wrote:
>> >>
>> >>> Jordi Huguet <[log in to unmask]>
>> >>> 4:58 PM (3 minutes ago)
>> >>> to SPM
>> >>> Dear all,
>> >>>
>> >>> I am trying to run CAT12 toolbox (r1450) in a HPC environment using
>> >>> the
>> >>> standalone SPM version (SPM12 r7478) for Matlab MCR R2018b.
>> >>> However, my first attempt at running it for segmenting a single
>> >>> image (via
>> >>> 'cat_batch_cat.sh' script) did not succeed. See log file content
>> >>> below:
>> >>>
>> >>> ----------------------------------
>> >>>> Sat Jun 15 16:16:36 CEST 2019
>> >>>> ----------------------------------
>> >>>> Calling string of this batch:
>> >>>> /opt/packages/spm/12-r7487/spm12_mcr/toolbox/cat12/cat_batch_cat.sh
>> >> -fg
>> >>>> -nojvm -nojvm -m -m spm12 /home/jhuguet/scratch/cat12/INPUT/mri.nii
>> >>>> MATLAB command of this batch:
>> >>>> cat_batch_cat('/tmp/cat_185160','')
>> >>>> Shell command of this batch:
>> >>>> /home/jhuguet/scratch/cat12/INPUT/mri.nii
>> >>>> nohup: ignoring input
>> >>>> Error using spm_cli (line 56)
>> >>>> Cannot find module -nodisplay.
>> >>>> Error in spm_cli (line 56)
>> >>>> Error in spm_standalone (line 157)
>> >>>
>> >>>
>> >>> Any ideas of what am I missing or doing wrong?
>> >>>
>> >>> Many thanks,
>> >>> Jordi
>> >>>
>> >>
>> >>
>> >>
>>
>
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