Advice for optimizing subcortical signal with phased-array head coils?

[dvsmith]

Thanks! This is very helpful to see. There’s still some chatter on the twitter link, so I wanted to return to this post and share what we had at this stage. Here’s a link to our OSF page (in progress): OSF

One thing that I learned while looking into this issue is that it looks like many people recommend using the pre-scan normalization option with this phased-array head coils.

Common persistent EPI artifacts: Receive coil heterogeneity

http://dbic.dartmouth.edu/pipermail/mrusers/2017-February/005997.html

This does seem to do a good job with making the images look better (more homogenous), but we had some masking issues with FMRIPREP with those runs, which can be seen for some of the task-rest data for sub-103 and sub-104. The FMRIPREP folks are using those data to make their approach more robust. (Thanks!)

ICA-AROMA error in FMRIPREP: 'Mask and image must be the same size'

Success! Thanks for the quick fix. Let me know if you still want examples for the pre-scan normalization. I’m seeing the same masking issues with those data, but it’s unclear to me whether it’s a quirk with those acquisition settings.