clowdcontrol / mindcontrol

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

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

In a browser navigate to localhost:3000

Configure

For configuration tutorials, see the mindcontrol_docs repository: http://github.com/akeshavan/mindcontrol_docs and the tutorial jupyter notebook: http://nbviewer.jupyter.org/github/akeshavan/mindcontrol_docs/blob/master/Installing_mindcontrol.ipynb

For an example Freesurfer editing instance of Mindcontrol, see http://nbviewer.jupyter.org/github/akeshavan/mindcontrol_docs/blob/master/MindPrepFS.ipynb

To see an example schema, see this file: https://dl.dropboxusercontent.com/u/9020198/data/data_rf.json

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

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

• 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

• You can log curves

• Edit voxels:

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

mindcontrol's Issues

Permission issues

There are some issues related to permissions for the mounted .mindcontrol volume (the -v ${PWD}/.mindcontrol/:/home/mindcontrol/mindcontrol/.meteor/local part of the docker command). Here is the error and situations where it occurs:

docker run -ti --rm \
-v ${PWD}/.mindcontrol/:/home/mindcontrol/mindcontrol/.meteor/local \
-v ${PWD}/credentials.csv:/home/mindcontrol/credentials.csv \
-v ${PWD}/credentials:/home/mindcontrol/.aws/credentials \
-v ${BIDS_DIR}:/bids \
-p 3000:3000 -p 8080:8080 \
clowdcontrol/mindcontrol:v${version}

...

/home/mindcontrol/.meteor/packages/meteor-tool/.1.3.3_1.grqrzh++os.linux.x86_64+web.browser+web.cordova/mt-os.linux.x86_64/dev_bundle/lib/node_modules/meteor-promise/promise_server.js:165 
      throw error;   
            ^                                                                                                  
Error: EACCES, mkdir '/home/mindcontrol/mindcontrol/.meteor/local/isopacks'

• If the .mindcontrol directory doesn't exist before running the docker command, docker creates it as root. When the container is running, it calls meteor as user mindcontrol, but that user can't write to the root owned directory, and the error occurs.
• If the .mindcontrol directory exists, but is owned by any user except UID 1000, the same error occurs
• If the .mindcontrol directory exists, but is owned by user with UID 1000, it works...

Any thoughts on workarounds for this? I was able to get this to work locally/on AWS because my user is 1000, but most users out there wouldn't be user 1000