New set of checkboxes for visible features

[raamana]

some facial features may still be visible after defacing such as eyes and ears, it would be help capture additional info

[raamana]

hey @ericearl @arshitha, do you think the checkboxes below would suffice? Feel free to suggest others. cc @agt24

['Pass',
 'Fail',
 'Brain removed',
 'faCial features',
 'eYes visible',
 'eaRs visible',
 'Unique mark(s)',
 'something Else',
 "i'm Tired",
 'review Later']

[Arshitha]

Thanks Pradeep! Here's suggestion of check boxes with a couple of very minor modifications to your proposal

['Pass',
 'Fail',
 'Brain removed',
 'too much eYes visible',
 'too much eaRs visible',
 'too much Brow visible',
 'Unique mark(s)',
 'something Else',
 "i'm Tired",
 'review Later']

I think "too much Brow" is focused for our/DSST needs but rest are good prompts for general defacing QC. Also, I removed "facial features" since we are specifying eyes, ears and brow, which covers the more common points of under-stripping. I can help with this but I was wondering if we could document and provide a couple of examples for each category that's not pass or review later, so that users know what we mean by "too much ears" etc?

[raamana]

Good suggestions Arsh, I'll add the Brow visible. More words in option might make the checkbox too long wasting space.

if you could supply some examples to documentation, that would be great. Do you know how to work with ReST formatted documentation and gh-pages of a python repo?

[Arshitha]

It's been a while since I used ReST but it shouldn't be a problem to figure it out. Thanks, Pradeep. I'll try to get it done by next week!

[raamana]

Great, thanks Arsh.

Also, depending on your interest/skill in Python, it would be straightforward to integrate freeview in VisualQC, given it works on your system now. If you are interested in contributing, i can walk you through what needs to be done (simply a loop calling fsleyes and managing its behaviour correctly). It shouldn't take more than a day or two.

[Arshitha]

Sure, that sounds good but did you mean fsleyes or freeview? I haven't used freeview before but it shouldn't be too hard to figure it out.

[raamana]

LOL, my bad, I meant fsleyes :)

[raamana]

we will be imitating how the freesurfer module generated cortical visualization using freeview or tksurfer, but now using fsleyes -- rather straightforward to change command name and parameters: https://github.com/raamana/visualqc/blob/46ff96f680f27bf1221581c0696a11361b4582a7/visualqc/freesurfer.py#L342