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==========
Glossary
==========
.. glossary::
AFNI
AFNI_ is a functional imaging analysis package. It is funded by
the NIMH, based in Bethesda, Maryland, and directed by Robert
Cox. Like :term:`FSL`, it is written in C, and it's very common
to use shell scripting of AFNI command line utilities to
automate analyses. Users often describe liking AFNI's
scriptability, and image visualization. It uses the :term:`GPL`
license.
BSD
Berkeley software distribution license. The BSD_ license is
permissive, in that it allows you to modify and use the code
without requiring that you use the same license. It allows
you to distribute closed-source binaries.
BOLD
Contrast that is blood oxygen level dependent. When a brain
area becomes active, blood flow increases to that area. It
turns out that, with the blood flow increase, there is a change
in the relative concentrations of oxygenated and deoxygenated
hemoglobin. Oxy- and deoxy- hemoglobin have different magnetic
properties. This in turn leads to a change in MRI signal that
can be detected by collecting suitably sensitive MRI images at
regular short intervals during the blood flow change.
See the `Wikipedia FMRI`_ article for more detail.
BrainVisa
BrainVISA_ is a sister project to NIPY. It also uses Python,
and provides a carefully designed framework and automatic GUI
for defining imaging processing workflows. It has tools to
integrate command line and other utilities into these
workflows. Its particular strength is anatomical image
processing but it also supports FMRI and other imaging
modalities. BrainVISA is based in `NeuroSpin <http://neurospin-wiki.org/>`_, outside Paris.
DTI
Diffusion tensor imaging. DTI is rather poorly named, because
it is a model of the diffusion signal, and an analysis method,
rather than an imaging method. The simplest and most common
diffusion tensor model assumes that diffusion direction and
velocity at every voxel can be modeled by a single tensor - that
is, by an ellipse of regular shape, fully described by the length
and orientation of its three orthogonal axes. This model can
easily fail in fairly common situations, such as white-matter
fiber track crossings.
DWI
Diffusion-weighted imaging. DWI is the general term for MRI
imaging designed to image diffusion processes. Sometimes
researchers use :term:`DTI` to have the same meaning, but
:term:`DTI` is a common DWI signal model and analysis method.
EEGlab
The most widely-used open-source package for analyzing
electro-physiological data. EEGlab_ is written in :term:`matlab`
and uses a :term:`GPL` license.
FMRI
Functional magnetic resonance imaging. It refers to MRI image
acquisitions and analysis designed to look at brain function
rather than structure. Most people use FMRI to refer to
:term:`BOLD` imaging in particular. See the `Wikipedia FMRI`_
article for more detail.
FSL
FSL_ is the FMRIB_ software library, written by the FMRIB_
analysis group, and directed by Steve Smith. Like :term:`AFNI`,
it is a large collection of C / C++ command line utilities that
can be scripted with a custom GUI / batch system, or using shell
scripting. Its particular strength is analysis of :term:`DWI`
data, and :term:`ICA` functional data analysis, although it has
strong tools for the standard :term:`SPM approach` to FMRI. It
is free for academic use, and open-source, but not free for
commercial use.
GPL
The GPL_ is the GNU general public license. It is one of the
most commonly-used open-source software licenses. The
distinctive feature of the GPL license is that it requires that
any code derived from GPL code also uses a GPL license. It also
requires that any code that is statically or dynamically linked
to GPL code has a GPL-compatible license. See: `Wikipedia GPL
<https://en.Wikipedia.org/wiki/GNU_General_Public_License>`_
and `<http://www.gnu.org/licenses/gpl-faq.html>`_.
ICA
Independent component analysis is a multivariate technique
related to :term:`PCA`, to estimate independent components of
signal from multiple sensors. In functional imaging, this
usually means detecting underlying spatial and temporal
components within the brain, where the brain voxels can be
considered to be different sensors of the signal. See the
`Wikipedia ICA`_ page.
LGPL
The lesser GNU public license. LGPL_ differs from the
:term:`GPL` in that you can link to LGPL code from non-LGPL code
without having to adopt a GPL-compatible license. However, if
you modify the code (create a "derivative work"), that
modification has to be released under the LGPL. See `Wikipedia
LGPL
<https://en.Wikipedia.org/wiki/GNU_Lesser_General_Public_License>`_
for more discussion.
Matlab
matlab_ began as a high-level programming language for working
with matrices. Over time it has expanded to become a fairly
general-purpose language. See also: `Wikipedia MATLAB
<https://en.Wikipedia.org/wiki/MATLAB>`_. It has good numerical
algorithms, 2D graphics, and documentation. There are several
large neuroscience software projects written in MATLAB,
including :term:`SPM software`, and :term:`EEGlab`.
PCA
Principal component analysis is a multivariate technique to
determine orthogonal components across multiple sources (or
sensors). See :term:`ICA` and the `Wikipedia PCA`_ page.
PET
Positron emission tomography is a method of detecting the
spatial distributions of certain radio-labeled compounds -
usually in the brain. The scanner detectors pick up the spatial
distribution of emitted radiation from within the body. From
this pattern, it is possible to reconstruct the distribution of
radiactivity in the body, using techniques such as filtered back
projection. PET was the first mainstream technique used for
detecting regional changes in blood-flow as an index of which
brain areas were active when the subject is doing various tasks,
or at rest. These studies nearly all used :term:`water
activation PET`. See the `Wikipedia PET`_ entry.
SPM
SPM (statistical parametric mapping) refers either to the
:term:`SPM approach` to analysis or the :term:`SPM software`
package.
SPM approach
Statistical parametric mapping is a way of analyzing data, that
involves creating an image (the *map*) containing statistics,
and then doing tests on this statistic image. For example, we
often create a t statistic image where each :term:`voxel`
contains a t statistic value for the time-series from that
voxel. The :term:`SPM software` package implements this
approach - as do several others, including :term:`FSL` and
:term:`AFNI`.
SPM software
SPM_ (statistical parametric mapping) is the name of the
matlab_ based package written by John Ashburner, Karl Friston
and others at the `Functional Imaging Laboratory`_ in
London. More people use the SPM package to analyze :term:`FMRI`
and :term:`PET` data than any other. It has good lab and
community support, and the :term:`matlab` source code is
available under the :term:`GPL` license.
VoxBo
Quoting from the Voxbo_ webpage - "VoxBo is a software package
for the processing, analysis, and display of data from
functional neuroimaging experiments". Like :term:`SPM`,
:term:`FSL` and :term:`AFNI`, VoxBo provides algorithms for a
full FMRI analysis, including statistics. It also provides
software for lesion-symptom analysis, and has a parallel
scripting engine. VoxBo has a :term:`GPL` license. Dan Kimberg
leads development.
voxel
Voxels are volumetric pixels - that is, they are values in a
regular grid in three dimensional space - see the `Wikipedia voxel
<https://en.Wikipedia.org/wiki/Voxel>`_ entry.
water activation PET
A :term:`PET` technique to detect regional changes in blood
flow. Before each scan, we inject the subject with radio-labeled
water. The radio-labeled water reaches the arterial blood, and
then distributes (to some extent) in the brain. The
concentration of radioactive water increases in brain areas with
higher blood flow. Thus, the image of estimated counts in the
brain has an intensity that is influenced by blood flow. This
use has been almost completely replaced by the less invasive
:term:`BOLD` :term:`FMRI` technique.
.. include:: links_names.txt
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