Skip to content

Instantly share code, notes, and snippets.

View JohnGriffiths's full-sized avatar

John Griffiths JohnGriffiths

View GitHub Profile
@JohnGriffiths
JohnGriffiths / 'tvb-robot
Last active August 29, 2015 14:09
tvb-robot - controlling a bot with the virtual brain platform
(gist naming file. ignore)
@JohnGriffiths
JohnGriffiths / 'getyourboton_code
Last active August 29, 2015 14:09
Get your bot on code
(gist naming file; ignore)
from tvb.simulator.lab import *
import threading
import numpy
import time
import sys
from matplotlib.tri import Triangulation
from matplotlib import pyplot as plt
class SimThread(threading.Thread):

Dipy hcp dsi reconstruction error

====================================

I'm getting an error with dipy DSI reconstruction on HCP WU-MINN data.

It's a bit of a mystery as I've definitely got successful reconstructions using dipy with code very similar to this. But now I am getting the error below every time.

All the files are included in this gist to reproduce the error, apart from the DWI data (too big); that was simply data.nii.gz from subject 100307.

Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@JohnGriffiths
JohnGriffiths / looking_for_anterior_cingulate_cortex_in_tvb_connectivities.ipynb
Created October 11, 2018 22:00
looking_for_anterior_cingulate_cortex_in_tvb_connectivities.ipynb
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@JohnGriffiths
JohnGriffiths / gist-reveal.it-slides.html
Created March 5, 2025 06:22 — forked from ryanj/gist-reveal.it-slides.html
Gist-powered Revealjs slideshow presentations http://gist-reveal.it
<section id='hello' data-background-transition='zoom' data-transition='concave' data-background='https://ryanjarvinen.com/presentations/shared/img/broadcast_reveal_dark.png' data-state='blackout'>
<h1><a style='color:deepskyblue;' href='https://gist-reveal.it'>gist-reveal.it</a></h1>
<br/>
<h2 style='color:white;'>Gist-Powered</h2>
<h1 style='white-space:nowrap;color:white;'>reveal.js slides</h1>
<p><small style="background-color: rgb(0,0,0,0.35); font-style: italic; color: white;"> press F1 for usage notes </small></p>
</section>
<section id='revealjs' data-transition='concave'>
<h3><a href="https://revealjs.com/">Reveal.js</a> is a framework</h3><p><span>for crafting presentations</span><br/> <span class='fragment'>in <a href="https://revealjs.com/markup/">HTML</a></span> <br/> <span class='fragment fade-up'>and <a href="https://revealjs.com/markdown/">Markdown</a></span>
<aside class="notes">Oh hey, these are some notes. They'll be hidden in your presentation, but you can see them if you open