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mindcontrol

MindControl is an app for quality control of neuroimaging pipeline outputs.

Installation

Install meteor

curl https://install.meteor.com/ | sh

Clone this repository

git clone https://github.com/akeshavan/mindcontrol

start the server

cd mindcontrol
meteor --settings settings.dev.json

In a browser navigate to localhost:3000

Configure

Create a database json file similar to http://dxugxjm290185.cloudfront.net/hbn/hbn_manifest.json

  • The required key values pairs are name subject_id check_masks and entry_type.
  • Make sure name is UNIQUE
  • check_masks is a list with paths relative to a staticURL
  • Host your database json file on a server and copy/paste its url into the "startup_json" value on settings.dev.json
  • Define each module in settings.dev.json to point to your entry_type, and define the module's staticURL

Demo

Check out the demo. This data is from the 1000 Functional Connectomes Project

Things to do in the demo:
  • create an account by clicking sign in on the top navigation bar
  • click on a site (for example, Baltimore) to only show exams from that site
  • In the freesurfer table, click the select box to change the metric of the histogram

switch histograms

  • Brush the histogram to filter the table, which only shows freesurfer id's that match the brush range

brushing and viewing images

  • Save your filter by typing a name in the left text-box
  • Click 'reset' to undo the filtering
  • Click on a Freesurfer subject id to open a new window that shows the aparc+aseg file
  • Mark Pass, Fail, Needs Edits, or Edited, and leave some comments about the image. Click 'save'
  • You can log points

log points

  • You can log curves

log curves

  • Edit voxels:

edit voxels

  • (beta) You can collaborate on the same image:

collaborate