Dear Guillaume,
As you adviced, I re-compiled SPM12 containing LST (as well as vbm8,
since LST needs it to be present) in the toolbox folder.
My own compiled version of spm12 works well, but when I try to run LST I
get the following error message:
# --------------------------------------------------
------------------------------------------------------------------------
Running job #1
------------------------------------------------------------------------
Running 'PVE label estimation and lesion segmentation'
Item tools: No field(s) named
vbm8
Item tools: No field(s) named
vbm8
Item segment: Dependency 'VBM8: Estimate & Write: Label Images' could
not be added.
Item segment: Dependency 'VBM8: Estimate & Write: Bias Corr Images'
could not be added.
Failed 'PVE label estimation and lesion segmentation'
Error using ==> spm_jobman>fill_run_job at 474
No executable modules, but still unresolved dependencies or incomplete
module inputs.
In file "/home/abaci/.mcrCache7.14.1/spm_st1/spm12/spm_jobman.m" (???),
function "fill_run_job" at line 474.
In file "/home/abaci/.mcrCache7.14.1/spm_st1/spm12/spm_jobman.m" (???),
function "spm_jobman" at line 246.
In file
"/home/abaci/.mcrCache7.14.1/spm_st1/spm12/toolbox/LST/ps_LST_lesiongrowing_run.m"
(???), function "ps_LST_lesiongrowing_run" at line 38.
The following modules did not run:
Failed: PVE label estimation and lesion segmentation
Bye for now...
# --------------------------------------------------
This error is very strange, since the vbm8 and LST are both in the
toolbox folder, and also when I run the compiled spm12 GUI, I can run
vbm8 (meaning that it is present and spm recognices it).
If you have a hint it would be extremely useful since I cannot bypass
this and I have to run LST over a compiled version of SPM.
Best,
Le 16/07/15 14:39, Guillaume Flandin a écrit :
> Dear Nicolas,
>
> if you have the MATLAB Compiler, the simplest is compile the whole SPM
> with LST in the toolbox folder - there are basic instructions in the
> third item of the FAQ list:
> https://en.wikibooks.org/wiki/SPM/Standalone#Frequently_Asked_Questions
> (basically just call spm_make_standalone.m).
> I would not recommend letting the compiler find the relevant SPM
> dependencies for LST automatically as it will probably miss a number of
> functions.
>
> Best regards,
> Guillaume.
>
>
> On 16/07/15 13:22, VINUESA Nicolas wrote:
>> Dear Guillaume,
>>
>> First of all, thanks for your quick reply.
>> What I'm trying right now (it's taking a lot of time) is to compile some
>> matlab .m file that uses LST and putting SPM as a resource (that's why
>> it is also compiling SPM). Do you think this would work?
>> If it doesn't, is there any way I could compile SPM myself (this time
>> including LST in its toolbox path)?
>>
>> Best,
>>
>> Le 16/07/15 14:08, Guillaume Flandin a écrit :
>>> Dear Nicolas,
>>>
>>> this is a limitation of the standalone version of SPM - everything has
>>> to be compiled beforehand in order to run so third-party toolboxes
>>> cannot be installed post hoc:
>>> https://en.wikibooks.org/wiki/SPM/Standalone#Frequently_Asked_Questions
>>>
>>> If standalone SPM becomes popular, we might consider also providing a
>>> version containing compiled versions of the main contributed toolboxes
>>> (provided they don't alter the behaviour of SPM core functionalities,
>>> don't overshadow SPM functions or modify defaults, etc).
>>>
>>> Best regards,
>>> Guillaume.
>>>
>>>
>>>
>>> On 16/07/15 12:08, VINUESA Nicolas wrote:
>>>> Dear all,
>>>>
>>>> I've encountered myself facing a problem when using standalone version
>>>> of SPM. The problem is that I don't know how to add a toolbox (in this
>>>> case Lession Segmentation Toolbox - LST) and make it run correctly.
>>>> What i've done is to unzip LST to SPM_HOME/spm12_mcr/spm12/toolbox
>>>> (therefore I have SPM_HOME/spm12_mcr/spm12/toolbox/LST, as well as for
>>>> example: SPM_HOME/spm12_mcr/spm12/toolbox/DARTEL, etc...) and then run
>>>> the standalone version of spm (run_spm12.sh). What I get when clicking
>>>> in LST (on toolboxes in the GUI) is the following error:
>>>>
>>>> # --------------------------------------------------
>>>> ___ ____ __ __
>>>> / __)( _ \( \/ )
>>>> \__ \ )___/ ) ( Statistical Parametric Mapping
>>>> (___/(__) (_/\/\_) SPM12 - http://www.fil.ion.ucl.ac.uk/spm/
>>>>
>>>>
>>>> SPM12: v6225 13:04:09 - 16/07/2015
>>>> ========================================================================
>>>> Initialising SPM : ........Warning: Requested
>>>> Font Size 1451 is too large. Defaulting to 10
>>>> > In spm at 360
>>>> In spm_standalone at 51
>>>> done
>>>>
>>>> SPM present working directory:
>>>> /home/abaci/tmp/LST
>>>>
>>>> ~ - SPM12: LST toolbox --------------------------------------------
>>>>
>>>> Toolbox directory prepended to MATLAB path:
>>>> /usr/local/MATLAB/spm12/spm12_mcr/spm12/toolbox/LST
>>>>
>>>> ----------------------------------------- 13:04:22 - 16/07/2015
>>>>
>>>> ??? Error using ==> evalin
>>>> Undefined function or variable 'spm_LST'.
>>>>
>>>> Error in ==> spm at 1002
>>>>
>>>>
>>>>
>>>> ??? Error while evaluating uicontrol Callback
>>>>
>>>> # --------------------------------------------------
>>>>
>>>> If instead I try running LST via a batch file, I get the following error:
>>>>
>>>> # --------------------------------------------------
>>>>
>>>> /usr/local/ABACI/xnat/pipeline/catalog/VBM/resource/runSpm/runSpm.sh
>>>> batch LST_batch.m
>>>> SPM12 (6225): /usr/local/MATLAB/spm12/spm12_mcr/spm12
>>>> ___ ____ __ __
>>>> / __)( _ \( \/ )
>>>> \__ \ )___/ ) ( Statistical Parametric Mapping
>>>> (___/(__) (_/\/\_) SPM12 - http://www.fil.ion.ucl.ac.uk/spm/
>>>>
>>>> Item tools: No field(s) named
>>>> LST
>>>> Execution failed: LST_batch.mBye for now...
>>>>
>>>> # --------------------------------------------------
>>>>
>>>> Any help on this issue will be greatly appreciated.
>>>>
>>>> Best,
>>>>
>>
--
Nicolas VINUESA
Ingénieur d'études
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