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!

Thursday, March 8, 2012

New user training guide/FAQ

I've just uploaded a new user training guide/FAQ that we use at Berkeley to initiate newbies into the ways of the dark side. It is Siemens-specific, for a Trio/TIM.

As last time, the guide is a bit rough. Sorry for English-isms and typos. It's worth exactly what you pay for it. It's free. Use and abuse it however you like. It's a Word document so that you can reorder things, add your own notes, etc. I would appreciate constructive feedback, especially if you find mistakes or have suggestions to improve it, but there's no need to ask permission to use it, change it, replicate it, sell it...

The most recent version of the training guide/FAQ is available from this web page:

Locate the file attachment towards the bottom of the page, it's called 3T_user_training_FAQ_08Mar2012.doc. The most recent contents and a list of changes since the last version (April, 2011) appear below.

Caveat emptor.

The document is only a component of user training, don't expect to learn how to scan by reading it! Rather, use the tips to extend your understanding, refine your experimental technique and so on. Note also that this document is for a Siemens TIM/Trio (with 32 receive channels) and running software VB17. There may be subtle or not-so-subtle differences for the Verio and Skyra platforms, for software VB15, VD11, etc. so keep your wits about you if you're not on a Trio with VB17!

You may have local differences, e.g. custom pulse sequences, that allow you to do things that contradict what you find in this user guide. Talk to your physicist and your local user group before taking anything you find in this guide/FAQ too literally.

Finally, you wont find many (any?) references in this guide/FAQ. It's for the training of newbies, not a comprehensive literature review! If you are seeking further information on something I mention in the guide and you can't find a suitable reference yourself, shoot me an email and I'll do my best to point you in a useful direction.


Update Notes (8th March, 2012):

  • Updated with new operating modes available under software syngo MR version B17.
  • General tweaks to improve readability.
  • Further recommendations on using the 32-channel coil for fMRI.
  • Added a description of the new AutoAlign procedure, AAHScout.
  • Added a new section: “I have an existing protocol that uses the old AutoAlign (AAScout). How do I get and use the new AutoAlign (AAHScout)?”
  • Added a new section: “I want to add a new acquisition and acquire exactly the same slices as this other EPI acquisition I just acquired. How do I tell the scanner to do that?”
  • Extended the discussion on the relative merits of PACE versus using an offline realignment alone, in the section on the ep2d_pace sequence.
  • Fixed a typo concerning the slice ordering for descending slices.
  • Added a new section: “What is a field map and how does it fix EPI distortion?”
  • Added a new section: “I want to try to fix my distortion with a field map. What do I need to acquire?”
  • Updated the sections on partial Fourier for EPI, noting that Siemens simply zero fills the omitted portion of k-space rather than doing a conjugate synthesis.
  • Extended checklists.