Hi Alex,

We always recommend running FAST on untransformed images.
That is, on the originally acquired images, after running BET to remove
non-brain structure, but without applying any spatial transformations.
The reason that intensities change with transformation is that
is required to look-up intensities between the original grid points.

If you want to see your images in MNI space or to do the tracing in this
space then that is fine - just register the images, transform them to
MNI space, do any tracing in this space and then transform your
masks back into the original space.  To do this last step you need to
invert the transformation (use InvertXFM or convert_xfm) and then
make sure that you make a floating point output image (for the mask)
and rethreshold it to the desired value (near 0.5 keeps the size about
the same, near 1.0 will "shrink" the mask to leave only voxels which
overlapped greatly with the mask in the MNI space, and near 0.0
will "enlarge" the mask, including any voxels with even small overlaps
with the MNI-space mask).  Then, once you've rethresholded, you have
a mask in the original space, and can use this in conjunction with the
FAST output from native space.

Also, FAST works best when it has access to the entire brain (excluding
non-brain structures) so don't use it just on an ROI in case that was
something you were thinking of.  To get the amount of gray matter in an
ROI just multiply a binarised mask (that only contains 1's and 0's) of
ROI with the gray matter PVE output from fast and sum the output.

Hope this all makes sense.
All the best,

On Tuesday, July 13, 2004, at 02:36  am, Alex Fornito wrote:

> Hi all,
> I am doing manual tracing on some T1 images. I've used flirt to align
> them
> by registering the stripped T1 to the MNI template, and then applying
> the
> transform back onto the unstripped image.
> I've noticed that doing this changes the pixel intensities. Since I
> also
> want to segment these brains using FAST, I was wondering if you could
> tell
> me
> a - exactly why do the pixel intensities change?
> b - does this introduce some error when I last segment with FAST?
> Basically, if I trace regions on the unsegmented image, and then
> attempt
> to segment the grey matter within the ROI using fast will this be an
> adequate representation of the region's grey matter volume?
> Thanks for your help,
> Alex