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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