Hi Roland,
See inline replies below for a couple of answers. John will be in later
today and probably will know the remaining answers.
Donna
On 11/22/2007 05:31 AM, Roland Marcus Rutschmann wrote:
Hi again,
while working with the new caret version 5.5 I encountered some new (at least
to me) features that I have some questions to.
Preprocessing-question:
a) When I load a 1x1x1mm T1-nifti image with a q-form that has some angle to
it, the voxel-dimensions shown in caret are not 1x1x1 any more but eg
0.96x1.02x0.99. How is the image resample if I use Volume->edit
Attributes->resample.
-is it just a resampling in the 3 major dimensions or is the affine
transformation of the q-form used?
-would you recommend this kind of resampling in this case?
Don't know. I know AFNI's 3dresample and FSL's flirt are alternatives.
b) Rescaling-Wish: I use an unbiased T1-image that has a few outliers. What I
do now I only use voxels within a lower-upper threshold to rescale. Is there
some option within caret to do this? If not, I think it would be nice ;-)
VOLUME SCALE VOXELS 0 to 255 WITH PERCENTAGE OF MIN/MAX
caret_command -volume-scale-percent-min-max-255
<input-volume-file-name>
<output-volume-file-name>
<percent-minimum>
<percent-maximum>
Scale voxels so that they are in the range 0 to 255 but
map the first "percent-minimum" voxels to 0 and map the
last "percent-maximum" voxels to 255.
The "percent-minimum" and "percent-maximum" values should
range from 0.0 to 100.0. Setting the "percent-minimum" to
2.0 and the "percent-maximum" to 3.0 will result in the first
two percent of voxel values being mapped to zero and the last
three percent of voxel values being mapped to two hundred
fifty five.
c) Remark: I often have a discrepancy of search handles and topology report of
the surfaces (both telling me no handles euler=2) on one hand and the
volume->segmentation->topology report on the other hand. In the latter I
often find euler=1, handles=1
The volume: segmentation: topology report tells the truth, but sometimes
the handles are so tiny (e.g., two voxels kissing at corners) that you
can't see them on the inflated surface. I'm not sure how the surface
topology report works, but I'm not surprised it sometimes disagrees with
the volume one. Another common discrepancy is when Find Handles returns
nothing in all three slice planes, but the topology error report still
shows handles. This is because Find Handles can only find "within
slice" handles; handles resulting from voxels kissing at corners are not
detected by Find Handles.
But my motto is to proceed to flattening if I can't see any handles on
the inflated surface, and Find Handles can't find any, either.
d) Remark-Question: Segmentation volumes seam to be saved as float32 not
gzipped per default. Is there a reason for this?
Possibly because Wash U's "4dfp" format saves volumes this way, and our
very first guinea pigs when John added volume support were wustl.edu
users. If there's a way to specify that segmentation volumes be
gzipped, I'm unaware of it.
e) separate brain extraction question: Do you think a brain extraction eg with
bet before segmentation is help/harmfull?
It is most helpful as a preprocessing step to bias correction, which can
make a huge difference. Otherwise, its effect is minimal. Caret
successfully removes the eye/skull without brain extraction most of the
time; for the few times it fails, brain extraction may not solve your
problems, because the eye fat is probably the culprit, and brain
extraction may miss this, as well. Most of the time, it shouldn't do
any harm. Turn off eye removal if it does.
Sorry for the many questions but there's so much to explore in your wonderful
program.
Regards and Thanks,
Roland
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