getting started with ET

[Barbara Kreilkamp]

Dear Boris and Sarah!

Great work on the ENIGMA toolbox, I've started to get familiar with it.

Are there any plans to integrate the site-corrections into the toolbox?

I realized that for the ENIGMA toolbox a python version of at least 3 is needed. I also seem to be getting a kernel error when trying to plot Cohen's D on the cortical surface (below). I'm using spyder 3.8 and after googling I have reset spyder to factory defaults which results in an endless 'connecting to kernel...' message. Could this have something to do with my conda environments and have you seen this before?

Thank you,

Kind wishes,

Barbara

# Project the results on the surface brain
plot_cortical(array_name=CT_d_fsa5, surface_name="fsa5", size=(800, 400), cmap='RdBu_r', color_bar=True, color_range=(-0.5, 0.5))

# Error

An error ocurred while starting the kernel[IPKernelApp] WARNING | No such comm: de9f8b106f7511eb989815ce9976a460

[Sara Larivière]

Hi Barbara,

Thank you! 

I think eventually it might be nice to integrate site-correction, however I have no plans of doing this any time soon! I know you've been working on that recently so if you want to make a pull request, please do so! Help is always appreciated :)

Yes it needs python 3+, it's only been tested with py 3.7 I believe.

I haven't had that error but I use either pycharm or the terminal - will check this out this AM though and let you know :)

Some updates have been made recently (maybe in the last month) so if you cloned the repo a while back perhaps try:

cd /path/to/ENIGMA/
git pull

python setup.py install 

Sara.

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[Sara Larivière]

Hi again Barbara,

In my conda environment with python 3.7, I installed Spyder (4.2.1):

conda install spyder

and then ran the script from the RTD (see attached) and it worked. Perhaps try (1) git pulling to get the latest ENIGMA Toolbox version and (2) installing spyder through your conda environment... 

Hope this works :)

Sara.

[Barbara Kreilkamp]

Thank you Sara! I have tried those things, but have emailed IT now, as it doesn't seem that I have the rights to update some these tools...

Will let you know what we find out!

Cheers,

Barbara