# mindcontrol

**Repository Path**: arestrack/mindcontrol

## Basic Information

- **Project Name**: mindcontrol
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Apache-2.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2018-10-12
- **Last Updated**: 2024-08-08

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# 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](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](http://mindcontrol.herokuapp.com/). [This data is from the 1000 Functional Connectomes Project](http://fcon_1000.projects.nitrc.org/fcpClassic/FcpTable.html)

##### 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](http://dxugxjm290185.cloudfront.net/demo_gifs/histogram_switch.gif)

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

![brushing and viewing images](http://dxugxjm290185.cloudfront.net/demo_gifs/histogram_brushing_and_image_viewing.gif)

* 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](http://dxugxjm290185.cloudfront.net/demo_gifs/logLesion.gif)

* You can log curves

![log curves](http://dxugxjm290185.cloudfront.net/demo_gifs/logContour.gif)

* Edit voxels:

![edit voxels](http://dxugxjm290185.cloudfront.net/demo_gifs/dura_edit.gif)

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

![collaborate](http://dxugxjm290185.cloudfront.net/demo_gifs/syncedViewers.gif)