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.eduwrote:

...

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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