I guess Dr. Ress decided on that resolution in order to obtain the high resolution anatomies. It is a GE scanner and we are using an 8 channel head coil. 

On Tue, Feb 15, 2011 at 5:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
but who decided 0.7mm iso was the right setting for the scanner? Can you change that? what kind of scanner and coil is it?


On Tue, 15 Feb 2011, Evan Luther wrote:

Sorry about that! Hear they are.  The reason why we want .7 mm resolution is
because that is the resolution of the volume anatomies we obtain from the
scanner.

Thanks again!

On Tue, Feb 15, 2011 at 4:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:

can you load them with the -segmentation flag in tkmedit so I can see them
as a color overlay? And is there a reason you need 0.7mm data? That's why it
is *so* noisy

On Tue, 15 Feb 2011, Evan Luther wrote:

 Hey Bruce,

Here are the aseg and aseg.auto_noCCseg files. Our data is at a .7 mm
resolution.

Thanks!

On Tue, Feb 15, 2011 at 4:15 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:

 what does the aseg look like n that case? And what resolution is your
data?

On Tue, 15 Feb 2011, Evan Luther wrote:

 Hey Bruce,


I also do not understand why I could not use the aseg but if I do not
set
the noaseg flag I get a result like the picture I have attached where no
cut
is made. I have also attached a picture of the slanted cut. I am not
sure
why this occurred and also why it only occurred on one subject's
anatomy.

Thanks for the help!

-Evan

On Tue, Feb 15, 2011 at 2:21 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu

wrote:


 Hi Evan


can you send some coronal images showing where it is slanted? I also
don't
understand why you can't use the aseg. What resolution are you
acquiring
the
data at?
cheers
Bruce

On Tue, 15 Feb 2011, Evan Luther wrote:

 Hello All!


I am currently trying to create a high resolution anatomy by manually
changing some parameters throughout the recon-all process. I have
currently
hit a road block at the fill portion of the recon-all process. So far
I
have
tried this high resolution reconstruction on two subject's anatomies.
In
both subjects I used the flag -noaseg as well as seed points for the
CC,
pons, left hemisphere, and right hemisphere at the fill step because
otherwise the fill command would use the aseg file for seed points and
subsequently the hemispheres would not get separated at all.

Now here is the kicker, in one subject's anatomy this worked fine. It
split
the hemispheres down the middle without a problem. However on the
other
subject the cut between the hemispheres is slanted, assigning portions
of
the right hemisphere to the left. I do not know how to correct this
problem.
I have tried using different seed points and not inputting seed points
and
this has yielded the same results. Any suggestion?

thank you,

Evan Luther



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