Hi folks,
My apologies for a really basic set of questions but I discovered
that I've never thought much about the basis of the brain mask before
and now it's tripping me up...
If I understand correctly, in first level analyses the brain mask is
essentially generated by first motion correcting the 4D data, then
running bet on it (using the -F option), and then thresholding the
volumes at 10% and keeping only those voxels which were non-zero
across the time series.
When I do this with our data (1.5T Siemens, GE-EPI -- fairly standard
stuff), the mask has two problems:
1) it leaves in all the scalp and stuff surrounding the brain and
2) it leaves out individual voxels inside the brain.
In the first case, this seems to come from the fact that the bet ..
-F command uses a lenient idea of brain and then further dilates the
mask, which essentially includes the splodge surrounding the brain
(but it does a good job removing eye balls). I wondered why the
extra dilation step was included and whether it can turned off or modified?
For the second, the fact that -Tmin is used in the command to
generate the mask significantly increases the number of missing
voxels within the brain volume due to small head motions interacting
with areas of low intensity (ie small spaces such as the lateral
horns of the ventricles near the hippocampus or places where noise in
the data artificially reduced the signal at a single time point). I
was sure what the motivation for including the -Tmin option was -- is
it just to reduce the volume to 3D or is it serving a deeper purpose?
Finally, I wondered why the mask was generated in the current fashion
rather than simply using bet to strip out the rubbish (I mean, of
course, the essential non-brain material...) in
example_func.nii.gz? Ok, and finally for real -- whether there was a
method for ensuring that individual voxels within the brain were not
excluded -- that is, computing the surface and then accepting
everything within that volume as brain material? At the moment, CSF
is not masked out because it has a higher intensity in T2* images so
I can't see any reason not to just assume anything within the surface
is wanted.
I assume there are good reasons for these choices but I realized I
don't have any good idea what they might be.
Thanks, in advance, for your help!
Joe
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