Actually, this excerpt from http://www.brainvoyager.com/featurelist.htm
suggests that the AFNI +tlrc PALS surfaces (piecewise linear conversion
to true Talairach space) would be the closest match:
Talairach transformation is performed in two steps. The first step
consists in rotating the 3D data set of each subject to be aligned
with the stereotaxic axes. For this step the location of the anterior
commissure (AC) and the posterior commissure (PC) as well as two
rotation parameters for midsagittal alignment has to be specified
interactively. In the second step the extreme points of the cerebrum
are specified. These points together with the AC and PC coordinates
are then used to scale the 3D data sets into the dimensions of the
standard brain of the Talairach and Tournaux atlas.
If this is how registration was done for your data, then the AFNI +tlrc
method is very similar.
On 12/07/2005 08:37 AM, Donna Hanlon wrote:
Jay,
Re-analyzing using AFNI, FSL, or SPM seems like overkill if the main
goal is to map group results to PALS, but you could compare these
results to your BrainVoyager results. The learning curve for learning
a new fMRI analysis tool is pretty steep; if you have this kind of of
time, option (a) would make sense more for
compare-BrainVoyager-to-other-volume-analysis-software purposes.
Option (b) seems much more practical. My quick look at the
BrainVoyager vmr and fmr format pages led to the same conclusions as
John's: The VMR is easy, but the FMR is more complex. The Caret
wish-list is pretty crowded, so priority juggling is more of an issue
these days. Under the "Adding Import Filters" umbrella, I'd rank
DICOM before BrainVoyager FMR, but really this wouldn't solve your
problem, because your DICOM files are raw files -- not the
post-analysis statistical output volume maps, which is really what you
want to map to our PALS atlas (my interpretation of what you want to
do with Caret).
My general philosophy on file conversion is that each software package
should be able to import and export files in some neutral file format
(e.g., NiFTI), so that each vendor doesn't have to create
import/export filters for every other format out there. Caret can
import NiFTI; find out whether BrainVoyager can export files as
NiFTI. Analyze is another format (really what NiFTI was trying to
improve) for which many vendors provide export or save as features; if
BrainVoyager can't export as NiFTI, then perhaps it can export as
Analyze. I'd be really shocked if it didn't support at least one of
these export options. There may be command line utilities (or batch
support) for such file conversion, so you don't have to convert each
file one at a time. I happened to come across this link while
searching for brainvoyager vmr, but I can't vouch for its quality:
http://grommit.lrdc.pitt.edu/fiswidgets/fisdocs/docs/FormatConvert.html
But even once you get past this hurdle, then the next issue you'll
face is which PALS surfaces to use for mapping purposes. Here are the
existing "spaces" or volume registration methods currently supported:
http://brainvis.wustl.edu/help/pals_volume_normalization/
The BrainVoyager VMR page
(http://www.brainvoyager.com/BV2000OnlineHelp/BrainVoyagerWebHelp/mergedProjects/FileFormats/whskin_homepage.htm)
says "The mapping to Talairach axes is as follows," but it would take
a while for me to figure out if what they're calling "Talairach" is
actually like one of our existing grids (e.g., MNI305, MNI152). I
doubt it will be like the AFNI +tlrc grid, but without doing a fair
amount of research, I can't be sure.
Do some sniffing around your BrainVoyager distribution
directories/folders. Look for volume files that look like they might
be an atlas target volume (e.g., named like talairach, mni152,
avg152T1, icbm*). Send me the names of any files named like that, and
it may give me some clues.
Ideally, there would be a magic option in BrainVoyager like "Export
files as NiFTI in mni152 space." ;-)
Donna
On 12/06/2005 02:04 PM, John Harwell wrote:
Jay,
The only Brain Voyager file format we read at this time is the
Surface File format.
This web site describes the BrainVoyager formats: http://
www.brainvoyager.com/BV2000OnlineHelp/BrainVoyagerWebHelp/
mergedProjects/FileFormats/whskin_homepage.htm
The VMR file looks fairly simple to read and the FMR looks more
complicated as it references STC files that appear to be like VMR
files. Are there any options in your version of BrainVoyager to
export to non-BrainVoyager formats such as Analyze of NIFTI?
Modification of Caret to read these files is possible, but this is
probably something you, myself, and David should discuss.
If there are other Caret user's who would find import of these
BrainVoyager files into Caret useful, please let us know.
It may be possible to use AFNI's "to3d" program to convert the files
to AFNI format, but "to3D" is not a tool that I know how to use.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Dec 6, 2005, at 12:19 PM, Jay Hegdé wrote:
Hi Everyone,
I'm BrainVoyager user (on a Windows 2000 machine), and a
total newcomer to Caret. I have a general question about how best
to port my functional and anatomical data into Caret.
Here's my overall situation: My study is revealing a pretty
larger number (>40) of highly reliable foci all over the cortex,
and I'd like to map them to a good surface-based atlas so as to (a)
assign them to Broadmann area/s, and (b) compare them reliably to
previous reports of activation, so as to discern the potential
functional significance of these foci. It looks like Caret is
right for the job.
Since Caret expects the volume data in a non-Brainvoyager
format (e.g., AFNI, SMP, etc), I need to decide whether to (a)
start over with my raw DICOM files in AFNI/SPM etc and process them
until they're ready for Caret, or (b) use my existing BrainVoyager-
format files (*.vmr, *.fmr etc) and find some way of converting
them into a format that Caret accepts.
So does anyone know which (if either) of the above
strategies is workable? I figure there must be some Caret users
out there who have grappled with this problem. Any advice you can
provide would be useful.
Thank you very much in advance,
Jay Hegdé
University of Minnesota
[EMAIL PROTECTED]
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