Hi Christine
if you upload this subject we will take a look
cheers
Bruce
On Thu, 30 Jan 2014,
Christine Smith wrote:
Hello,
The parcellation of grey and white matter appears to be off in several
T1-weighted structural scans I have been processing. The effect is observed
in the temporal lobes, parietal lobes, and part of the occipital lobes. The
frontal lobe does not seem to be affected as much.
For example, the medial white matter is super white, while more distal white
matter near the cortex is less white (grey). Grey matter itself is rather
dark (black in some cases). If you monkey around with the brightness of the
image you can see that, for example, the pial line has actually followed the
distal white matter and not the grey matter. Moreover, the white matter line
has followed the boundary between medial (super white) white matter and more
distal (greyer) white matter. This effect is most pronounced in the temporal
and parietal lobes nearest the brightest parts of the white matter across
the entire scan. About 3-5 voxels are cut off. For the frontal lobe and
caudal occipital lobe, though, it is only cutting off about 1 voxel around
the edge of the brain.
I have attached a picture of this problem with the pial and white matter
lines on the image. Look at the cortex in the lower left hand part of the
image (lateral temporal cortex). For the image called Missing_Voxels.tiff I
have adjusted the standard brightness of the image in freesurfer to show how
much of the brain we are missing. In the image called
Missing_Voxels_Brighter.tiff I have left the brightness levels as they
appear when you open freesurfer. The problem appears less severe in this
latter image because the standard brightness level has made some of the grey
matter appear black and it is easier to miss that it is actually present.
Now look at the top of the image and see that the pial line there is pretty
accurate, though it does appear to cut off maybe 1 voxel too much.
Extracting the eTIV from one of these scans shows that their intracranial
volume is much smaller than other participants whose data were obtained on a
different scanner. Also, each lobe volume is reduced. For example, the
parietal lobe is about 15 standard deviations smaller than a group of
participants scanned on a different scanner. These types of reductions are
observed if you include grey matter only and also if you include grey+white
matter in the calculation of the lobe volumes.
Thus, the problem appears to be that we are missing the most outer part of
the grey matter across a large part of the brain. I should also mention that
the skull itself is missing (on the T1 image) near the lateral temporal
lobes so there may be some signal dropout there. Though the lateral temporal
cortex itself becomes visible when the brightness of the scans is adjusted,
the skull in that area never does become visible.
Is there any way to fix this problem at a basic level in one of the earlier
steps of freesurfer?
I have tried putting in a bunch of control points in the "real" white matter
and it does make the white matter extend out further. However, the pial line
is still cutting off ~3-4 voxels of brain in the problematic areas.
Best,
Christine
--
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego
--
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego
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