[caret-users] Some remarks, whishes, questions

[Roland Marcus Rutschmann]

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?

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 ;-)

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

d) Remark-Question: Segmentation volumes seam to be saved as float32 not 
gzipped per default. Is there a reason for this?

e) separate brain extraction question: Do you think a brain extraction eg with 
bet before segmentation is help/harmfull? 

Sorry for the many questions but there's so much to explore in your wonderful 
program.

Regards and Thanks,

Roland

-- 
Dr. Roland Marcus Rutschmann <Roland.Rutschmann at psychologie.uni-regensburg.de>
Institute for Experimental Psychology, University of Regensburg
Universitätsstraße 31, 93053 Regensburg, Germany
Tel: +49 941 943 2533, Fax: +49 941 943 3233
http://www.psychologie.uni-regensburg.de/Rutschmann
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