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!

Tuesday, April 19, 2011

Administrative Post: 19 April, 2011 (2/2)

Siemens users may be interested in a user training guide & FAQ that we use at Berkeley to initiate newbies into the ways of the dark side. (Using the Force is often the only way to get an fMRI experiment to work. What, you thought the f stood for functional? Ha!)

The guide is a bit rough - sorry for English-isms and typos - is updated fairly regularly based on popular misconceptions and the like, and is 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_19April2011.doc. The most recent contents appears 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 VB15. There may be subtle or not-so-subtle differences for the Verio and Skyra platforms, for software VB17, VD11, etc. so keep your wits about you if you're not on a Trio with VB15!

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.


User guide/FAQ contents (as of 19 April, 2011):

What is the practical difference between the 12-channel and 32-channel head coils? Which one is best for fMRI?

I have a subject who has a lot of dental work. Is this person okay to scan?

Why does the scanner instruct me that the patient bed might move when I start the first scan in my session (usually a localizer)?

I can’t hear anything happening? How can I tell what the scanner is doing right now?

Why do I sometimes get a message that the subject might experience peripheral nerve stimulation? Should I tell the subject?

How does the AutoAlign feature work? Should I use it?

I don’t want to trust AutoAlign. How should I define my slice positions manually?

When does shimming happen and what is actually done?

I want to re-shim my subject’s brain midway through my session. How do I do it?

How do I know whether I should re-shim or not?

I want to know how long my scan will take. Where is the scan time shown?

What is the difference between the Scan and Apply buttons for starting a scan?

Help! What pulse sequence am I using?


I’ve been told not to use echo spacing between 0.6 and 0.8 ms for EPI. How come?

How many dummy scans happen before the first real (saved) volume of EPI in my time series?

I want 200 volumes in my EPI time series. How do I do that?

On the BOLD card, what is Motion Correction? How do I turn it on or off?

My protocol has TE set at 28 ms for EPI. But I saw somebody else’s protocol that uses a TE of 22 ms. How come?

I am using ep2d_bold. What are the specifics of using this sequence?

I am using ep2d_pace. What are the specifics of using this sequence?

I am using ep2d_neuro. What are the specifics of using this sequence?

What flip angle should I use for fMRI?

What TR should I use for fMRI?

Should I use interleaved or sequential slices for fMRI?

In what order does the scanner acquire EPI slices?


I hear a lot about ghosting when people talk about EPI. What is a ghost and what causes them? How do I get rid of them?

On the Contrast tab I notice that fat suppression is enabled for EPI. What does it do?

What is the origin of signal dropout in EPI? Can it be fixed?

What is the origin of distortion in EPI? Can it be fixed?

Whoa! I’m watching my EPIs on the Inline Display window and I’m seeing all sorts of weirdness. What’s going wrong?

How much subject movement is too much?


What the hell is iPAT? Last time I checked, grappa was a strong Italian drink! It makes no sense!

Is GRAPPA a good technique to use? What are the caveats?

What is “partial Fourier” and why might I want to consider it for EPI?

Is partial Fourier a good technique to use? What are the caveats?

It looks like I will need to use either partial Fourier or GRAPPA to get the spatial resolution and coverage that I want. Which method should I use?


I want to scan overnight. Is there anything I need to watch out for?

I hear we have a research agreement with Siemens. Why should I care?


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