Pradeep Reddy Raamana

Handle few deprecations in scipy

1

during CI on my [hiwenet](GitHub.com/raamana/hiwenet), I discovered a ton of deprecation warnings from scipy : https://travis-ci.org/github/raamana/hiwenet/jobs/658810855 mostly asking medpy to move from scipy to numpy for functions such as sum,...

Structure for the tests

10

Hi Maksim! Nice package, thanks for sharing! I am trying to use it and hoping to contribute. Before I use it, I'd like to understand how it is tested. For...

Reader for Freesurfer Morphometry stats

13

Hi Everyone, I need to read various volumetric (subcortical) and morphometry stats from Freesurfer output (e.g. SUB/stats/aseg.stats) https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Apologies if I haven't looked hard enough, but it seems nibabel doesn't...

Improved Defacing module (version 2?)

14

incorporating valuable suggestions from @arshitha @ericearl et al. fixes #59 #60 and maybe even #61 let's see :)

- possibly interface to XNAT server directly

New set of checkboxes for visible features

8

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

integrate fsleyes to generate rendered images for defacing module

8

```bash fsleyes render --scene 3d -rot 45 0 -30 --outfile tmp.99.result.deface.fsleyes.render_1.png tmp.99.result.deface.nii -dr 30 250 -cr 30 500 -in spline -bf 0.225 -r 100 -ns 500 ``` thanks to Arshitha...

to let user customize it for their dataset @ericearl

the `.add_alerts()` and `.update_alerts()` methods of various workflows are exact duplicates! they can absorbed into the `visualqc.base.BaseWorkflow` class without any loss of functionality and avoid duplicated code. However, this requires...