Johan Carlin

IPYNB_FIX_CSS nukes markdown table headers

1

Thanks for a great tool. I have a problem where markdown table headers disappear (they're there in the output source, but seem to get assigned 0 height). Here is an...

Running notebook on singularity

1

Has anyone managed to get the tutorial to run under singularity? I just did a pull and conversion with ```singularity pull docker://miykael/nipype_tutorial:latest``` There seems to be something funny about the...

the [CBU example scripts](https://github.com/automaticanalysis/automaticanalysis/tree/master/examples/cbu) demonstrate some really cool aa functionality that isn't really covered anywhere else, since we don't have much documentation. It's a shame that only people at CBU...

Inconsistent stream outputs between segment8 and dartel_normmni

4

I had a meeting with Rik today and learned that the VBM pipeline includes a conversion of tissue probabilities to volume. Sometimes you want one, and sometimes the other. In...

aa user group

5

The AA user group is currently referenced in the README. It's very quiet. This doesn't look good for project activity. Should we a) retire it, b) commit to using it...

aap.spm can no longer be modified in user script

1

as of #205 aap.spm only appears in the aap struct in aa_doprocessing, which means users can't set custom SPM defaults in the user script without running afoul of aamod_checkparameters. Is...

PCA output option in aamod_compSignal

2

[aamod_compsignal](https://github.com/automaticanalysis/automaticanalysis/blob/master/aa_modules/aamod_compSignal.m) outputs a mean time course for each ROI. However, a large region (e.g., all of white matter) may not be well described by a single time course. So Rik...

More standards-compliant code formats?

2

I just started working on the code, and it's a little tricky to get used to some of the non-standard conventions, especially the super-deep indentation. Would it be worth running...

At the moment it's quite possible for neurconda.yml to be stale with respect to neuroconda_basepackages.yml. It might be better to drop neuroconda.yml from the repo entirely, and consider it a...

At the moment we unnecessarily invoke the solver when installing the environment from neuroconda.yml. The environment is already constructed to be solvable, and all versions are pinned, so this step...