Dear Jonathan and Volkmar,
Yes, best would be to take this up with the author of the toolbox.
Looking at the first dependency in your pipeline and describing how it
can be fixed:
* tbx_cfg_LST.m: the "Lesion segmentation (LGA)" module calls
ps_LST_lga() and describes dependencies in tbx_cfg_LST/vout()
* tbx_cfg_LST/vout(): the 'Lesion probability map' dependency is
obtained from a 'lpm' field.
* ps_LST_lga.m: change the last line so that it reads:
varargout{1} = struct('lpm',{{fullfile(pwd,Vles.fname)}});
This would require more work to make it robust but I hope it explains
how dependencies can be fixed. You would then have to do something
similar with tbx_cfg_LST/vout_lesthresh() and ps_LST_thresholding.m
Best regards,
Guillaume.
On 11/02/2021 13:02, Volkmar Glauche wrote:
> Hi Jonathan,
> I have had a quick look into the code of the LST toolbox. Guillaume has already named the issue: While there is code that tells the batch system which outputs can be expected (tbx_cfg_LST.m - this is why you can use them in the batch GUI), there is no code in the functions called at runtime (ps_LST_lga.m, ps_LST_lesfill.m and ps_LST_thresholding.m) that would actually create the output variables and fill them with contents. As you noticed, the files are created on disk, but the filenames are not passed on to output variables. It would require some MATLAB programming to modify the toolbox functions to return the filenames.
> Best,
> Volkmar
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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