April 2020 - update
Remi Gau
Hey all,
I hope that that you and your relatives are well in these dark times.
I am taking some time to give you an update on COBIDAS checklist project.
OpenMR hackathon
First of all a few of us worked on the project at the hackathon during the openMR event that happened at the Donders at the end of January. We mostly started creating boilerplate text in view of having the eCOBIDAS app automatically generate the method section of a paper for the users who could be interested by such a feature.
The boilerplate section would have empty spaces to be filled in by the app with the choice made by the user when filling in the checklist. For example for slice timing:
Slice timing correction was implemented in [stc_software] ([stc_version]) and applied using [stc_method]. Individual slices were realigned with slice [stc_reference] as a reference. As interpolation method, [stc_interpolation] interpolation was used.
Another thing that we worked on was starting to list the option choices and identify the default options of some common softwares. For example SPM and FSL might not offer the same type of cost function or interpolation method for realignment. The extreme case being when a software only has 1 option (e.g slice timing interpolation for SPM). Knowing this might help us reduce the number of options or questions that the user is exposed to: this could potentially speed up how long it takes users to fill in the checklist.
Finally quite a few people involved in high field and high resolution MRI were present at openMR were interested to see how well such a checklist could be used and extended to fit the need of this emerging field. The idea being to set good reporting practices as early as possible. I should meet (virtually) with a few of them early May. Let me know if you are interested in joining.
I still need to do some cleaning on what was produced at this event but currently it all lives in this folder: https://github.com/Remi-Gau/COBIDAS_chckls/tree/master/boilerplate
OHBM poster
I totally forgot to get back to you on this but the abstract that was submitted at OHBM A) got accepted, B) was accepted as a software demo. So yay! :-)
Not sure exactly what format this will take given that OHBM is going virtual this year but this could be interesting.
BrainWeb
Next weel there will be an attempt to start running a virtual hackathon. The initiative is called BrainWeb. Feel free to drop by virtually and say "hi".
I will take that opportunity to join and take some time to wok on the checklist. So also feel free to come and ask questions if you want to chat about and / or help with the project.
Take care and stay safe.
Rémi