Jeff Browndyke wrote:
> What tracing software for the creation of anatomical masks best
> works with SPM2 or SPM5? And, does anyone know of a primer, good
> methods paper, or workshop for how to implement this anatomical
> ROI/non-atlas approach in SPM2 or SPM5?
Hi Jeff. We have a tool called vbview (part of our VoxBo package,
www.voxbo.org) that you may want to try out. It lets you draw on
multiple planes, but not (yet) on 3D rendered surfaces. It
reads/writes both analyze and nifti formats, which should make it
compatible with SPM2 and SPM5. One reason I mention it is that we're
currently funded to extend it for lesion-behavior analysis. This
isn't the same thing as fMRI analysis in patients, but it's likely any
features you need will be things we're motivated to add quickly.
vbview does not directly help with ROI analyses in SPM (it does so in
VoxBo), but is designed to be functional as a stand-alone sketching
tool.
One minor complication: we are just a few days away from a new
release, and the old version probably won't quite meet your needs.
However, if you'd like to take a look (or if anyone else is
interested), I can put a pre-release Linux binary up later today. We
also expect to have OSX, Win(Cygwin), and maybe Solaris/SPARC
binaries, trailing the Linux release by about a week. There are also
command line utilities in the package, including one that implements
some of the inter-rater reliability metrics described in Fiez et
al. [] (originally proposed for lesions, but could certainly be used
for ROIs), as well as various utilities for image and mask munging.
All this stuff is GPLed, and none of it uses your MATLAB licenses.
vbview is also helpful for casual surfing of 4D time series data,
either for single voxels or averaged withtin ROIs.
> My previous SPM experience has been confined to normal anatomy, so
> what we're hoping to do is a bit foreign right now. I want to do
> the right thing with this data and warping to the SPM template
> doesn't seem to be it. I know manual tracing will be a major pain,
> but I don't see any other way to work around the atrophy/function
> issue.
Manual tracing is a rewarding activity, in every possible way -- well,
except the tedium. But if your number of ROIs is in the single digits
or close, I'd encourage you to think of it as an opportunity to
convert pain into knowledge.
dan
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