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Streamlining MEG data project blog

Megstream system evaluation results

User Avatar Aston MEG 29/09/2010 14:24:21
It seems like a long time ago, but back in July we ran an evaluation workshop for the Megstream system using a questionnaire to help understand end-user satisfaction with the software.

Workshop participants - all existing MEG users - completed two questionnaires: one for the existing system and a one after using the Megstream software. They were asked to rate their experience of using each system by selecting descriptive words from a randomly-ordered list.

The results for each system are presented as a word cloud above.

As you can see, the contrast between the experience of using the two systems is incredibly clear.
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Megstream final project progress post

Aston MEG 06/09/2010 09:57:33
Megstream: Streamlining the processing of MEG data
The Megstream prototype aims to simplify brain research and make it more accessible. MEG scanners measure magnetic activity in the brain over time. Specialist software from the vendor produces images of this activity within the brain for analysis and diagnosis.

The Megstream software makes it easier to produce these images by:

overlaying the previously complex and ‘fuzzy’ process with ordered workflows.
providing remote access to these analysis workflows via a web browser
 
And it makes it easier to track and reproduce the underlying research by:

recording information about each scan in a database
using a plugin to the WordPress blogging platform to link the information in the database and the process of creating and analysing MEG images

Project screencast
View the project screencast


End User of Prototype
The Megstream system was designed with students, new MEG users and clinicians in mind, but its data tracking system may also be useful for research groups, joint research partnerships and supervisors.

For students and other new users, workflows simplify the previously complex process of producing images of magnetic brain activity by automating some of the repetitive and complicated tasks involved. Workflows make the system less daunting allowing users to focus on their research rather than the tools they’re using.

Remote access to the workflows means that MEG users can process and view their data from anywhere that has a Java-enabled web browser and internet connectivity. This opens MEG techniques out to wider audiences regardless of location. For example, clinicians in hospitals could use MEG even though it may not be available locally.

For students, supervisors, research groups and joint research partners the database and blogging software provide a way to easily track and manage scan data and its outputs over time.

Students can augment or replace their paper-based notebooks with blog posts directly linked to the data they’re using. The posts are related to one another through the use of ‘tags’ and build up into a complete record of the work done. This could provide the basis for an electronic portfolio and even link into institutional repositories.

Using WordPress’s RSS feeds, supervisors can remotely monitor the progress of students, engage in online discussions about their work in situ, and prompt and intervene where necessary.

Research groups and partners can collaborate and discuss work using the blog knowing that it is a central store for all the project information. Workflows ensure that the same protocols and procedures are used by the partners across their sites.

End user documentation
http://code.google.com/p/megstream/wiki/Documentation

Code repository
http://code.google.com/p/megstream/

Date prototype was launched
July 2010

Project Team Names, Emails and Organisations
Ian Holliday i.e.holliday@aston.ac.uk – Aston University
Caroline Witton c.witton@aston.ac.uk – Aston University
Craig Everitt c.a.everitt@aston.ac.uk – Aston University
Project manager astonmeg@gmail.com – Aston University
Andrew Stanczak a.stanczak@aston.ac.uk – Aston University

Project Website
http://www.aston.ac.uk/megstream

PIMS entry
https://pims.jisc.ac.uk/projects/view/1584

Table of Content for Project Posts

Development sprint reviews
Sprint 9 review
Sprint 8 review
Sprint 7 review
Sprint 6 review
Sprint 5 review
Sprint 4 review
Sprint 3 review

Project Board
Megstream Project Board Meeting
Second Megstream Project Board meeting summary
Megstream Project Board mid-project meeting
Final Megstream Project Board

Conference presentations
Streamlining the processing of MEG data accepted for Human Brain Mapping 2010
Human Brain Mapping 2010: Megstream poster
Megstream at Virtual Research Environments Workshop in Rotterdam
Virtual Research Environments Workshop conference report
HBM 2010 conference report

External collaboration
Preparing for clinical feedback
Learning about MEG metadata from MRI
Metadata magic from the Digital Curation Centre
Multi-site MEG study meeting
Making MEG data more available and usable
Demonstrating Megstream to other MEG sites

Workflows
One workflow to rule them all
Accessing Taverna remotely
Whizzy workflows
Taverna's annoying workflow diagram repositioning
MEG process documentation used in neuroimaging teaching
Megstream workflows now available on myexperiment

Project analysis and evaluation
Project evaluation take 1
Megstream Swot analysis and the move to development
Initial project Swot analysis
Understanding data structures
Analysis complete, now development begins
MEG data process
Megstream software evaluation process
Megstream software evaluation first thoughts
Megstream system evaluation results
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Megstream software evaluation first thoughts

Aston MEG 22/07/2010 16:12:27
I'm just back from a very positive Megstream software evaluation workshop. The work that we've done was well received. The new system created a lot of energy for the process and there were good suggestions for extensions to the project. There'll be a full write up and posting of the findings in the coming weeks.
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Final Megstream Project Board

Aston MEG 21/07/2010 12:14:47
The final Megstream Project Board is scheduled for Wednesday 28th July. The outline agenda is shown below and a full report will be posted on the blog after the event. 
  1. Human Brain Mapping and Virtual Research Environments conference reports
  2. Final progress report.
  3. Project software demonstration.
  4. Final project sign-off work
  5. Project post-partum
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Megstream workflows now available on myexperiment

Aston MEG 12/07/2010 15:10:04
Ian Holliday's started the process of uploading the Megstream Taverna workflows to the myexperiment.org website. You can download the first one - CTF - MEG Event Averager - now.
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Virtual Research Environments Workshop conference report

Ian E Holliday 30/06/2010 16:30:20
On 23/24 June Ian Holliday attended a meeting organised by the Knowledge Exchange. 'Knowledge Exchange is a co-operative effort that supports the use and development of Information and Communications Technologies (ICT) infrastructure for higher education and research.' sponsored by JISC (UK), DFG (D), Deff (DK) Surf foundation (NL). Details of the workshop are available here http://www.knowledge-exchange.info/Default.aspx?ID=389 including podcasts by speakers on the day.

I was surprised by the breadth of contributions to the workshop - I had imagined it was going to be mostly software designers talking about new XML methods for stuff I'd no idea about. In fact it was mostly people working in social sciences and humanities settings, applying methods of collaborative working to help research teams in their discovery efforts.  there were some fascinating things going on, including a project to enhance digitisations of textbook concerning machines - potentially very old books - by animating the technical drawings on the digitised page in the style of the original drawings.

Closer to our project was one presented by Mathias Razum of Fachinformationszentrum Karlsruhe on eSciDoc. TThe thing that caught my attention here was that they have more or less the same problem as us, but concerning outputs from a very large mass spectrometry system. The eSciDoc solution seems very sophisticated, and aims to be a general purpose solution to problems of providing provenance and sustainability for large data-centric research platforms.  I talked quite extensively to Mathias about their system in comparison to our solution. One key difference is that they use XML Fedora to provide the database compared to mySQL. Mathias thought XML offered a lot of advantages - we should maybe explore eSciDoc further. One great feature was that QR codes can be printed off for each data acquisition/analysis procedure and stuck in the researcher's paper notebook. When this is later scanned, all the relevant material is retrieved from the database. How cool is that?
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HBM 2010 conference report

Ian E Holliday 30/06/2010 16:04:10
The 16th Annual Meeting of the Organization for Human Brain Mapping took place in Barcelona 6-10 June and Ian Holliday went to present the Megstream developments at the meeting. The presentation was a poster exhibited over two days with three sessions when attendees could meet with poster presenters. The abstract of the poster is now available via the meeting website at: http://www.aievolution.com/hbm1001/index.cfm?do=abs.viewAbs&abs=3863. There were quite a few other presentations with the theme of improving data management, 'streamlining' processing, and other means by which the research process in brain imaging could be made more robust, easier for new researchers to enter, and provide greater potential for data re-usability and data provenance. Some of these were advanced custom designed platforms, and of these 'MEG -Clinic' seemed to be the most advanced. The poster abstract can be seen here http://www.aievolution.com/hbm1001/index.cfm?do=abs.viewAbs&abs=4546.

As in our project these authors identify the same need to overcome processing the bottleneck in MEG analysis and aim for an automated workflow. Certainly MEG Clinic needs to be evaluated alongside our solution. To my mind though, the simplicity and robustness of our approach has a lot to recommend it. We cannot offer at present solutions to users of non-CTF scanners and this is a problem for potential adopters of Megstream. In the wind-up of the project we will see how expertise in Taverna programming can be sustained by the MEG research team beyond the end of the project, so that we can look forward to supporting Megstream workflows on the new Elekta system that will be commissioned in the next year or two.
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Sprint 9 review

Aston MEG 25/06/2010 15:30:05
The work packages for this sprint were:

• Create a web-based interface for adding the extra scan metadata
• Build a plug-in to link the CTF database to a WordPress installation

Create a web-based interface for adding the extra scan metadata
The additional database that was specified in Sprint 8 is now complete. The front-end form to allow MEG users to add and edit their scan metadata is working on a local machine. You can see the details of the interface (including a nice little feature to allow users to quickly add the most used terms) in the image above right. The database and front-end will be transferred to the live system next week as part of the remaining integration work.

Build a plug-in to link the CTF database to a WordPress installation
The plug-in has been completed and the scan metadata is automatically added to a new blog post when completed. The system also generates a unique ‘tag’ that is used to link all the posts about a particular study. This tag will be used to create the top-level directory structure for the study. This should allow for easy retrieval of the datasets, associated commentary and final results. Using WordPress’s built-in features to create an RSS feed of the tag will also enable interested parties to keep up to date with the study. The key use case for this would be Supervisors and PhD students.

As this is the final development sprint the remaining work is integration, testing and reporting. This will be completed on a continuing basis with the following primary workpackages:

Run evaluation sessions for the project work completed to date As I posted on Wednesday, we’ve started the process of recruiting students and new MEG users for informal sessions to judge the usability and utility of the work that we’ve done. The evaluation sessions themselves are scheduled across the next fortnight.
Complete project prototype screencast and final blog post
Move metadata recording systems from local machines to live servers

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Megstream software evaluation process

Aston MEG 24/06/2010 14:51:20
As the final phase of the Megstream project approaches we’re working out the process for evaluating the work that’s been completed. As a preliminary to this we’ve recruited a group of student and clinical users to help us. These people have varying degrees of experience using the current system and they’ll be asked to do a relatively standard usability evaluation:

1. They’ll use the system (with their own data and studies or datasets that we’ll provide) following the documentation that we’re currently writing.
2. We’ll observe and question them whilst they’re using the software.
3. Finally, the users will complete a questionnaire to measure their satisfaction with the system. These responses will provide the basis of a post-test guided interview that will summarise their experience using the software.

A summary of the findings will be posted on the blog. As well as providing feedback on our performance, they'll be used to improve future versions of the Megstream software and possibly feed into similar projects.
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Megstream at Virtual Research Environments Workshop in Rotterdam

Aston MEG 23/06/2010 12:50:09
Having been to HBM in Barcelona, Ian Holliday's rolling up our Megstream poster again and heading out to Rotterdam for the Virtual Research Environments - The Next Steps workshop. He'll be writing up the conference and the workshop for the blog so expect to see his reports here in the next few weeks.
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