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Issue N° 02.2008
Analyzer 2 in practice
Analyzer 2 – Redefining workflow oriented EEG analysis
by Ingmar Gutberlet, Ph.D., Customer Support Manager
With the public Beta phase now having come to an end and with
the final release of BrainVision Analyzer 2.0 only a couple of weeks
away, it is high time for us to take a look at some of the things we
have implemented in Analyzer 2.0 that will make all of our “EEGLifes” much easier.
Basically, in my book there are two things that are most important
in making an EEG analysis tool a Winner: The first is the user
interface and the second is the analysis workflow.
Its revolutionarily easy and powerful workflow was what made
Analyzer 1.x so successful, so the sights were automatically set
very high when we tackled Analyzer 2.0. Still, as we all know, even
the best can always be improved upon and this also held true for
the workflow in Analyzer 1.x.
The graphical interface in Analyzer 1.x was solid in functionality
and quality, but admittedly not nearly as revolutionary as the
workflow concept, so the need for improvements in Analyzer 2.0
was obvious and we aimed at no less than a complete rewrite of all
things graphical in Analyzer 2.0.
Figure 1
Of course, and in fact first and foremost, this also pertains to the
graphics output, but for this Press Release, I will have to limit
myself to the graphical interface of BrainVison Analyzer 2.0. I will
revisit the massively enhanced graphics abilities of Analyzer 2.0 in
the next Press Release article on this topic.
But as always, let’s take things step by step. I will start with the
new features of the graphical user interface in Analyzer 2.0.
Workspaces and Work-Spaces …
First things first: You will not have to learn anything radically new
in order to continue your work with Analyzer 2. The three-pane
interface is right there if you want it to be and the History Tree
concept is also in place. But upon closer inspection you will find
that many things small and large have changed and some of those
you can already see in the figure 1.
For one thing, you may notice that the History Explorer as well as
the “Navigation Bar” have little push pin symbols next to their also
new close buttons. In both cases these push pins are pointing
downward in a “pushed” fashion and consequently their windows
stay on screen just as they did in Analyzer 1.0. However if the push
pin is clicked, the respective window will subsequently only stay
visible for as long as the mouse hovers over it and will otherwise
vanish towards the window margins, thus increasing the amount
of screen usable for the data display.
This makes good sense in light of the number of channels steadily
increasing and also since more and more visualization tools are
being added in Analyzer that
need space to show their data.
Having e.g. the History Explorer
on screen while these data
visualization tools are shown
would restrict the visible
data space too much for the
display to be efficient. Below
is a view of the data interface
maximized automatically, with
all three tool windows “folded”
away. Figure 2 nicely shows the
advantage in this.
As you can see, the Navigation
and Toolbox windows are
tucked away to the bottom and
to the right, giving you maximal
space on screen for the data
you really want to visualize.
However, both can instantly
be reactivated by placing
the mouse cursor over their
respective titles. This may seem illogical at first for the Navigation
bar, since a folded away Navigation does not allow – Navigation
-, but this can still make a lot of sense. If you, like me, prefer
to navigate with the keyboard shortcuts for moving and scaling of
the data, then you would only need the navigation bar whenever
you wish to navigate to some specific part of the data or check the
location of some markers. Then, having a navigation bar take up
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Issue N° 02.2008
List” shown on the right comes
into play. This “Node List” is
a component of the History
Explorer, which now shows the
Primary and Secondary History
Files in two tabbed windows
and the Node List is shown in a
third. You can see the tabs used
to select the primary, secondary
or history node list data at the
bottom of the figure 3.
Figure 2
valuable desktop space all of the time does not make much sense:
Need it, point at it…
The History Node List shows the
names of all open windows and
above this list you can see a
number of options. The first, on
the left, is the “Group” option,
which allows you to group your
nodes by the file they belong to
or by their transformation type
or by their status, which could
be “hidden” or “shown” (see below). As you can see, I chose to
The “Toolbox”, which you can see tucked away at the right hand
window border contains several useful tools for graphically
annotating figures. While these tools are nice to have around, they
are of course not constantly in use and can therefore fold away
while staying available for easy access with one point (i.e. not a
“click”, just a “point”) of the mouse.
The window element that frees up the most space when tucked
away is of course the History Explorer and again I hear you mumble
“Wonder if that makes sense, I use it all the time”. All I can say is
“try it, you’ll love it”. The movement in and out is fast and smooth
and the navigation within the tree is no different from the push pin
“stay mode” with the only difference being that you retain much
more space on screen. And before I forget to mention, the data
window does of course not rescale every time the windows move
in and out. Instead, they are overlaid with the tuck-away windows
for the time these windows are active.
Another thing you can see in the above figures is the window title
above the data window, which looks like a label tab on a file folder
and this is quite right.
In the past it could prove challenging to navigate the many open
windows that were typically created during a “heavy” work session.
The first step towards changing this situation is that open windows
are not hidden behind the active window, but instead are listed on
the title bar and can be selected much easier. You can also simply
grab the window titles and move them around on the title bar, thus
giving you the ability to sort your windows in the order you want to
work with them.
But this would admittedly not be enough to help when working
with many windows and this is where our new “History Node
Figure 3
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Issue N° 02.2008
sort my history nodes by the history files they belong to.
The next option, “Sort” allows you to specify a sort order for your
nodes. This can be the natural (alphabetic) order I have chosen
here, it can be by depth within the respective history files or it
can be a “recursive” sort order. So, what do the latter two actually
mean?
Depth means that you wish to sort the nodes by the order in
which they appear in your History Files. If, for instance, you have
an Average node and its Standard Deviation node open for four
experimental conditions, then choosing Depth would show you
those four Averages first in the node list, followed by the four
Standard Deviations, because the Standard Deviation nodes are
deeper within the History File structure than the Averages.
Recursive on the other hand would honor the fact that the Average
and its Standard Deviation belong together and are neighboring
node. It would therefore show them in this order and for the four
sets Average/Standard Deviation separately underneath one
another.
It is evident that these two options alone will allow you to now
finally use your open datasets to their full advantage and needless
to say the search order you specify is instantly copied to the main
data window’s data order, but there is more…
The “Search” option lets you search within your open data windows
and the first entry to match the search criterion is highlighted
dynamically, meaning that the search is already being executed as
you type. Want to find the next or further entries that match? No
problem, just hit the Return key and the next entry is searched for
and highlighted.
The “Filter” option takes this one step further. Only window paths
that contain the alphanumeric text you enter here will then be
displayed in the node list until you remove the filter condition.
But let’s say you wanted to concentrate on this Averages and
Standard Deviations and hide all other history nodes. As you
can see in the figure above, each entry has symbols for “Close”
and “Minimize” on the right. Thus, simply click on the Minimize
button for any file to hide it from the display view completely or
close it by clicking “x”. Windows that are closed are of course
removed from the list, but minimized windows can be displayed
again by again clicking the button. Want to close or minimize many
windows at once? Simply mark them with the mouse using the
Figure 4
classical Windows methods to select ranges of entries (Shift-Click)
or specific but nonetheless multiple entries (Ctrl-Click).
As you can see, this History Node List alone is a powerful addition
to the workflow concept of BrainVision Analyzer, but – you guessed
it – there is lots more.
But before we go further on into the topic of workflow changes, let
me give you a last point on the user interface.
With more and more Transformations being added to Analyzer,
the “Transformations” menu was bursting the boundary of the
screen and we had to come up with a way to manage the growing
complexity of this and other menus.
After some discussion we finally decided to adopt the so called
“Ribbon” menu structure introduced by Microsoft with their Office
2007. Figure 4 shows you an example of what this looks like in
Analyzer 2.0.
We realize that this looks like a big change to make at first, but
nearly all of the people we asked about their experience with this
menu concept in Office 2007 said that it does indeed take a little
bit of getting used to but that you learn to love it very soon. This
encouraged us to employ this concept in our brand new Analyzer
2.0 – Now or never… - But please also note that we will initially not
have icons for the many, many entries in all of our menus, which
means that all of the menus will benefit from the grouping that
are possible now, but will still have more or less text based menu
items. We will of course add icons for all transformations, but we
want to take our time with this so we do not (necessarily) end up
showing a coffee filter for … guess which of our Transformation.
Granted, it would be obvious, but would it also be befitting?
There are many, many more changes at the User Interface level that
I could show and go into details on, but I would rather like to spend
the remaining space of this article highlighting just a few of the
many Workflow improvements we implemented in Analyzer 2.0.
Pending nodes or “Go to lunch when you feel like it…”
Do you know this situation: You would love to go home or to
lunch, but you are right in the middle of a semiautomatic Ocular
Correction and have a mere 700 blinks left to check, so it’s “diet
time” because Analyzer 1.x does not allow you to temporarily pause
and later resume an operation once started? Sure, you could press
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Issue N° 02.2008
OK and finish prematurely, but this is not the same, since Analyzer
would later only see the work you had done so far and “resuming”
would effectively mean restarting.
This has now changed with the introduction of what we call
“pending nodes” in Analyzer 2.0. For most of the more time
consuming semiautomatic operations you can now specify that
you want to pause the current operation instead of finalizing it.
There will be a History Node created, but its name will be shown
in red ink denoting the fact that this node is “pending”. Resuming
the pending operation is then done by double-clicking on the node
and Analyzer will take you exactly to where you left off. Nice…
That’s basically already all there is to it, but this concept inherently
also means that you are no longer locked into the operation you
are currently working on and this also means that you can now
leave the operation you are currently doing to do something else
without any ill consequences to what you have done so far at all!
A good example for this is the new ICA based Ocular Correction,
so let’s assume that the ICA components returned give you the
feeling that there must be some artifacts hidden in the data that
you did not see before but would have wanted to remove before
doing the ICA. So, you want to go back to a previous data node
and run a Raw Data Inspection to test for this. While this was not
possible in Analyzer 1.x because the ICA would have to be finished
before you could do anything else, this is easy in Analyzer 2.0.
Simply activate the desired previous node, do your thing and then
return to the ICA based Ocular Correction. That’s it!
quick and efficient. However, this situation is quite different if you
wanted to change some integral parameter in an MR correction or
ICA decomposition, since rerunning a large ICA with the changed
parameters could easily take hours and then there were those
nodes below that could only be dragged and dropped once the
new node had been created. Not so nice…
Well, fear no more, we have installed two routines that now allow
the editing of Transformation parameters in History Files as well
as in History Templates. These are “Edit parameters / Reprocess”
and “Edit parameters / Copy” and the first option reprocesses
the changed parameters and all subsequent nodes in place
while the second option creates a new branch starting with the
changed history node and then copies the subsequent nodes to
the changed one. This second variant would for instance come in
handy if you need to replicate the Segmentation step many times
to account for all of your experimental conditions but want to have
all the subsequent processing done in the same way. You would
then only have to change the segmentation parameters, while all
the rest is taken care of automatically.
So, what’s next in line…
As you can well imagine, this is but the tip of the iceberg of great
new feature small and large we implemented in Analyzer 2.0, but
since this a press release article and not a manual, I have to stop
here and give you a rain check for the next press release.
Alternatively you could pick up you own copy of Analyzer 2.0 as
soon as it is released and explore the possibilities yourself, right?
Delete me, delete me not…
Have you ever deleted a node, or worse, a branch or full tree in
Analyzer by clicking an automatic “yes” to the safety question
presented? – Well, I have and it wasn’t fun, because there was
not way back to the previous state of things. We knew you would
like a change to this, so we implemented unlimited Undo ability in
Analyzer 2.0.
If you now accidently delete a node, branch or tree, simply rightclick and choose “Undelete Child Node” and up comes your most
recently deleted node or branch. Small feature, but endlessly
useful and a potential life saver as well.
“Change and Drag” is now called “Edit and Watch”…
One of the most frequently requested features was the ability
to change parameters of Transformations in History Files or in
History Templates in place without having to run the respective
Transformation again with the desired parameter changes and
then dragging and dropping all of the nodes underneath to the
one changed Transformation.
In the simplest of all cases this would essentially have been the
same as editing the parameters in place, because redoing the tobe-changed step and copying the subsequent ones would be so
Solutions – Ready to go…
All of the Solutions currently available can be found ready for
download on our website but more are in the pipeline and will be
added constantly. And, if there is something that you and possibly
many others would love to have in Analyzer, let us know.
Download, double click and restart Analyzer if it was already started
and you will find the new module in its corresponding category
in the “Solutions” menu. All of our solutions contain online
information on their function and parameters, readily accessible
via “Solutions Help” and a double-click on any of the entries.
Please note that the use of Solutions requires Analyzer version
1.05 or better. If you are still working with an earlier version of
Analyzer, please consider upgrading. See our website for a free
download of the newest version of Analyzer and any updates or
addition of new analysis modules that may be available. The most
current version of Analyzer available is 1.05.0005, but great things
are coming your way, so look out for Analyzer 2.0 …
For questions, comments or suggestions on Solutions or regarding
problems that could use one, contact Ingmar at support@
brainproducts.com.