Expanding Mindcontrol - collaborative web based viewer for QC and editing FreeSurfer recons

[Remi-Gau]

Expanding Mindcontrol- collaborative web based viewer for QC and editing FreeSurfer recons

Anisha Keshavan, Lee Tirrell, and you?

FreeSurfer is the most widely used software for modeling cortical surfaces, capable of providing a complete neuroanatomical description of the brain from T1 weighted images through both surface based and volume based processing streams. However, manual invervention is necessary to QC results or when certain stages of the pipeline fail, especially when analyzing pathological brains. When analyzing large datasets this process may become error prone. To help organize inspection and editing of FreeSurfer output among collaborators, Mindcontrol was developed as an open source web-based tool for quality control of neuroimaging pipeline outputs.

During this brainhack, we aim to extend Mindcontrol in the following ways:

• Create a Docker container encapsulating all of the components of Mindcontrol, to make it easier to deploy.
• Continue development of Nipype workflows to automatically prepare FreeSurfer output to be viewed within Mindcontrol.
• Create workflows to re-run various FreeSurfer processing steps after manual inteventions have been made in Mindcontrol
• Extend documentation to make it easier for other users to set up Mindcontrol for their own data