No get_curvature in utils

[andrewolaughlin]

This is similar/identical to jcolquitt's Display only curvature as we're working together on the same thing

I'm trying to get curvature and thickness into the data layer of my rois.svg

rois.py has from utils import get_curvature, add_roi

this doesn't work in ipython, naturally as utils has no such function

in freesurfer.py there is a get_curv

is this what roipack.to_svg is supposed to be calling?

[jamesgao]

Ahh, that's a good idea -- I should add the curvature and thickness directly when the rois.svg file is first created. In the mean time, you should be able to add them using these commands:

import cortex
curvs = cortex.DataView(cortex.surfs.getSurfInfo("S1", "curvature"), cmap="gray")
cortex.add_roi(curvs)

Replace "curvature" with "thickness" for thickness rendering.

As for the utils, there's a separate utils module from within pycortex. Technically, that import is incorrect, so thanks for the bug report! The correct way to retrieve curvature from pycortex is using cortex.surfs.getSurfInfo. This will compute the curvature if it is not found, and cache it for quick loading in the future. Most of the functionality in cortex/utils.py is one-off computation, and probably doesn't need to be accessed by the end user.

As for creating an svg, you might want to try cortex.quickflat.make_svg.

[alexhuth]

We should also add sulcal depth to SVG file by default. It's really useful for finding some sulci (IPS).