Obtaining movement estimates before slice time correction

I was wondering if it is possible to obtain movement estimates before slice time correction.

Based on the workflow in the fmriprep documentation, it looks like slice time correction is done before head motion estimation. Is there any way to reverse this order?

I ask this because there were some concerns recently raised that using slice time correction first may artificially reduce motion estimates (http://www.sciencedirect.com/science/article/pii/S1053811917302288, p. 176). Does anyone know If this is possible, or if an option is planned for future releases?


Yes, we actually had a chat with J. Power shortly after the paper came out and we wanted to do this change. I’ve formalized this request in a new issue, and we’ll try to prioritize it: https://github.com/poldracklab/fmriprep/issues/849

Thanks for the suggestion.

I improved the description of the issue. It seems like a perfect way to get involved in the project. @jordan_theriault would you like to submit a pull request with this improvement? We can help you along the way.

I saw that this is in the new version! Thank you for including this, and sorry that I wasn’t able to help hack it out. I’m a bit new to Python, so may not have been a ton of help just yet. I will look out for opportunities to help out and return the favor in the future though!