Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Monday, May 18, 2015

Checklist for fMRI acquisition methods reporting in the literature: version 1.3

The latest version of the fMRI acquisition checklist is now available at The Winnower via this link. It can also be located/cited using DOI: 10.15200/winn.143191.17127 .

Updates/changes from v1.2:
  • The “Pre-scan normalization” parameter has been renamed “Signal intensity correction/normalization” to broaden its scope.
  • Reviewed and revised explanatory notes.
  • New parameters: RO partial Fourier scheme, Number of echoes, Saturation bands, Gradient non-linearity correction, Z-shim gradient correction, On-resonance adjustment.

The current list should work now for most simultaneous multislice (SMS) EPI, multi-echo EPI (or spiral) and 7 T experiments, but additional emphasis will be placed on these advanced methods in the next round. Please let me know of parameters you'd like included. The next planned update will include as far as possible the vendor-specific nomenclature for each parameter. I anticipate a late 2015 release date. There are no plans yet to do a machine-readable version of the checklist, as originally discussed, but that is only because nobody has been asking for it. Please get in touch if this is something you're interested in.

Thursday, May 14, 2015

Uploading to The Winnower from Blogger: A real time tutorial

So I have a memory like a sieve except that it's profoundly less useful in the kitchen. And because I know from painful experience that anything I don't document never happened, I am going to help myself and you by creating in real time a tutorial to upload blog posts from Blogger to The Winnower, should you be so inclined. Why do it? DOI is one reason.

Those of you who were smart enough to begin your blog's existence on Wordpress can use a fancy plugin for your API. Those of us who now have too much inertia on Blogger to relocate must do a little more work and use some intermediate steps, but it really isn't that hard. What's more, the intermediate steps offer an opportunity for proofreading and fine-tuning that you might like to do anyway. Let's do it!