pycortex

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Inconsistent handling of nans by WebGL viewer for Vertex vs. VertexRGB objects

2

We known that NaNs are not handled well by the WebGL viewer for `Vertex` objects. However, it seems that the viewer can handle NaNs perfectly fine for `RGBVertex` objects. We...

mvdoc

cortex.quickshow TypeError and ExpatError

1

Hello, I'm trying to plot a flatmap and can't seem to get past quickshow. I've been following code from the example gallery; (https://gallantlab.github.io/pycortex/auto_examples/datasets/plot_volumeRGB.html#sphx-glr-auto-examples-datasets-plot-volumergb-py - but same problem with other examples)...

EllieMo

Feature-request/bug: Pycortex readout of new fmriprep format

1

Dear Gallantlab, I would like to use pycortex on a dataset already preprocessed by fmriprep. Until now, pycortex adheres to the old path structure with a derivatives directory containing an...

ChristianNSchmitz

ValueError with fmriprep dataset

4

Dear pycortex-team, we are trying to use the pycortex software on an fmriprep dataset. However, the adapted example of the tutorial results in the following error. Thus, we would like...

ChristianNSchmitz

Viewer fails to load surface shader for cortex.Vertex object in Firefox

2

The following code fails to load the surface shader in Firefox (both 81.0 and 82.0a1). ```py import cortex dataset = cortex.Vertex.empty(subject="S1", vmax=1) cortex.webshow(dataset) ``` Interestingly, the following **does work**: -...

TomDLT

Is it possible to change the transparency(opacity) of main brain surface?

1

In the mriview.js and mriview_surface.js of webGL viewer, Is there any variable can be change the opacity of main brain surface? The transparency menu of UI only seems to change...

iPsych

MNI subject key error, so how to AAL atlas or other MNI space ROIs?

1

Hi everyone~ I want to ouline the AAL atlas as suggested in #170, but when I tried vol = cortex.Volume('aal116MNI.nii.gz', subject='MNI', xfmname='identity') I got the MNI key error. I check...

willanxywc

add_cutdata seems to overwrite data for left hemisphere with data from right hemisphere.

1

Hi pycortex. I seem to have uncovered an issue that doesn't seem to have been raised so far. It overlaps somewhat with https://github.com/gallantlab/pycortex/issues/398 ### Problem To illustrate this problem clearly,...

N-HEDGER

Add documentation on colormaps

1

As suggested in https://github.com/gallantlab/pycortex/pull/395#issuecomment-870054614, we could have some section on the pycortex documentation page that organizes the colormaps somehow, maybe something like how they give lists of "perceptually uniform", "sequential",...

TomDLT

bumpy flatmap fixes

3

To (~) productively procrastinate from writing, I fixed some issues with the bumpy flatmap rendering. First let me remind y'all what the point of bumpy flatmaps is. FLATMAPS ARE HARD...

alexhuth