Hi Catherine

can you clarify? Are you getting them properly segmented in the aseg? Is this a disease population? There are a bunch of things going on in the images you sent, although it's hard to be sure from a single slice. It looks like your bandwidth is low enough that you are getting a lot of signal pileup in temporal regions. There also appear to be cortical lesions.

Bruce

On Thu, 10 Jan 2013, Catherine Bois wrote:

Ps. I have attached a few screenshots of the problem we are experiencing, to clarify. We are also getting large areas of hyper-intensive white matter too.

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu on Wed, 9 Jan 2013 08:52:08 -0500 (EST):

...

Hi Catherine

what version are you running? We have a fix in 5.2 that helps this problem. It's not quite out yet, but you could download a beta if you want

cheers Bruce

On Wed, 9 Jan 2013, Catherine Bois wrote:

...

Hi,

I am currently editing some scans (ie adding control points etc), however I keep finding that after the editing often the brains look "worse" than they did before; especially the medial temporal lobe area. I have taken care not to put too many control points in/made sure not to place them in partial volume areas, and only in areas that are clearly excluded white matter. This problem has happened repeatedly, yet looking at scans that my colleagues have edited (some with up to 2000 control points) this problem does not occur. Has this happened before, is it the software "malfunctioning" in some way?

Thank you very much for your reply,

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