PR161 + review - #163

I do the same (demo and BIDS) here, at the RHUL.

All went well on my end.

aa_user_diffusion crashes for me during aamod_diffusion_rois_dartel_denormDKI. I am a little stumped here. regstreams is defined as inptstreams(1:end-3), which means it is what? Then we iterate over that and drop any where aas_stream_hascontents returns zero. And we end up with nothing. I don't really understand what this code is trying to achieve. Can you reproduce the error? I think it's something to do with the ROI input stream.

        imreslice{1} = aas_getfiles_bystream_multilevel(aap,domain,[subj sess],regstreams{end});
Error in aa_feval (line 15)
    [varargout{:}]=feval(funcname,varargin{:});
Error in aa_feval_withindices (line 4)
[aap,resp]=aa_feval(mfile_alias,aap,task,ci{:});
Error in aa_doprocessing_onetask (line 185)
            [aap,resp]=aa_feval_withindices(mfile_alias,aap,task,indices);
Error in aaq_qsub_debug (line 42)
                aa_doprocessing_onetask(obj.pool.Jobs(eii).Tasks.InputArguments{:}) 
87          imreslice{1} = aas_getfiles_bystream_multilevel(aap,domain,[subj sess],regstreams{end});

I have found the issue and debugged it. Try again, please!

Thanks, that seems to have done the trick.

Shall we merge, then?

Still running through the tests. I accidentally tested the wrong version so having to rerun a few things.. Stay tuned.

Now we crash on aa_user_freesurfer (old aa_user_FS), which is trying to define subjects with a 1-argument approach and crashes on undefined varargin{2}. Do we still support this call syntax? Maybe we need to set directory_conventions.

aap = aas_addsubject(aap,90952);

I have updated the example script.

aa_init lines 77-79:

clear ft_defaults
clear global ft_default
ft_defaults;

This code worked fine for us under previous versions of Matlab.

Under R2018a, it crashes on line 79.

This feels like a typo. On the other hand, it's related to fieldtrip initialization and we don't use fieldtrip.

Are you sure it is the MATLAB version? I am using 2018a in multiple places without issue.

I'll doublecheck (might be a mac/linux thing)

For my own understanding, what does line 79 (ft_defaults;) do?

https://github.com/spm/spm12/blob/master/external/fieldtrip/ft_defaults.m

But why clear it?

To remove previous (potentially conflicting) settings (e.g. from another version of SPM)

Update: Ok, today it is not crashing.

If it starts crashing again, I will update.

Ok, I have managed to get through the test suite. Merging...

I pushed one more commit (cc2e390) to the repo - turns out my shell expansion method only works in bash, and the rest of CBU is on tcsh. All fixed now. Sorry not to do another pull request, but this was a hot fix - AA was basically broken for all non-bash users.