Interested in fMRI but not Associated with
an fMRI Lab?
Using the CNL Website
Overview of the fMRI experiment
Interested in fMRI but not Associated with an fMRI Lab?
If you are a graduate
student or faculty member and you think you'd be interested in running your
own fMRI experiment, you need to be willing to make a huge time and energy
commitment. Here are some reasonable steps to follow if you think you are
1) Review the work of
the following principal investigators:
Elena Plante, and
Elena Plante, and
From the information
you glean there, decide who you want to approach about a project.
Presumably, your proposed project will be closely related to projects of
the researcher you choose to talk to. That investigator can help you decide
how best to proceed.
If you are a graduate
student, and just want to learn what is involved running an fMRI
project consider approaching one of the four researchers above about
volunteering to help in their lab working on an MRI or fMRI project.
Using the CNL Website
magnetic resonance imaging) experiments have to be designed and tested
behaviorally before you put someone in the magnet (i.e., MRI machine).
After you put someone in the magnet, you have a bunch of images to move
around, reconstruct and analyze. You'll need people to help you get started
with this process, but the CNL website can be a reference when you want to
learn more or you are stuck on terminology or "how to" issues.
Glossary: The most important page on the CNL website is the
glossary. You'll find an alphabetized list of definitions, with links to
other pages and even some standard references for software (since you'll
need to reference the software when you write papers). If you want to look
up a term, try the glossary first. If you don't find a term that you are
looking for, please email me (firstname.lastname@example.org)
Search: If the glossary fails you or you can't figure out
how we referenced something, try the search.
Links If you want background
information, MRI and fMRI theory, image processing theory, neuroanatomy
etc., you should consult the Links page.
you think a topic has been discussed on the Imaging Analysis listserv, then
Analysis archive search. This will sometimes address technical issues,
but usually addresses meetings, machine status etc.
Overview of the fMRI
If you have a
background in designing good behavioral experiments, then you are well on
your way to designing good fMRI experiments. fMRI experiments are very
expensive to run, so avoid using them as fishing expeditions. If you run an
experiment first as a behavioral experiment, and you get clear results AND
there is a good reason to see what lights up in the brain, then talk to one
of the CNL researchers listed above about setting up a pilot project. Be
prepared for a lot of issues you didn't think of at this point.
Subjects: Subjects must meet certain
criteria to enter the scanner (they can't have metal in their heads, they
shouldn't be claustrophobic, they have to be able to lie still while you
scan, they can't be pregnant etc.). The CNL has standard questionnaires
about relevant issues. See the forms page
metal screening form, materials you can provide to subjects and
instructions on setting up equipment and subjects at the magnet.
The Experiment: How will you present your
experimental stimuli? Timing is important, so we usually automate
presentation, and you must decide between
block design and
event related design. The
length of each functional scan is typically between 2 and 15 minutes, with
an image volume gathered every 2 seconds. You may wish to run 2 or more
functional scans on each subject (e.g., scan them doing a task before
and after some experimental manipulation). You probably don't want
to make anyone lie there for more than 1.5 to 2 hours total. Typically, we
create visual and/or auditory stimuli (see the
that run on a computer and are presented to the subject via headphones
and/or goggles. Subjects can provide feedback by pressing buttons on mice
(we have two mice, so they can hold one in each hand). It is difficult to
have subjects talk, because they might move their heads if they talk (a bad
thing) and the magnet is very noisy....but you can have subjects think
about something, and then try to tell you about it later. For some
specialized studies, eye tracking hardware and software are available.
the Magnet Setup:
You'll have to know something about neuroanatomy. The details of how you
set the scan parameters depend on what area of the brain you want to image
well and the structure of your experiment (unfortunately, there are always
tradeoffs. Some brain areas are easier to image than others, and some brain
areas are better imaged in a particular orientation). Issues you'll need to
worry about at the scanner are, at least,
TR, slice thickness,
and number of repetitions. Typically, for
each subject you will collect some number of functional scans, and two anatomical scans (a T1 "2D" image and a 3D image).
Save the Data: You will want to transfer
your data from the console to mrisun (a linux workstation at UMC). There
you can either burn the data to CD or, if you have permission from the CNL,
you can have access through mrisun's firewall so you can transfer data to
another machine. Instructions for transfering data are here. Instructions for burning data to a CD on
mrisun are here. Keep in mind that
your data is very valuable and copies will NOT be kept indefinitely on the
console. If your data gets mangled in the transfer, doesn't get transferred
correctly or the CD is messed up, it is gone forever. Our standard protocol
has always been to copy data from one machine to another rather than moving
it, to burn 2 cds of the data and keep them in separate places, and to look
at the data as soon as possible, to make sure there are no problems. The
console machine is sgi and mrisun is linux. These are both distributions of
unix. If you are unfamiliar with unix, consult the
Process the Data: There are a number of image processing and analysis programs for
looking at your data. You will need to choose one. A wide variety of
programs are used by CNL researchers. SPM and Afni are two of the most
common. Tutorials on SPM block-design analysis and on
Afni block design analysis
are available online. As
you begin to do analysis, you may want to know something about images. The image properties page may be very helpful.