The output says that the voxel size is .7031, .7031, 1.5 (slice thickness is 1.5). Could this be causing the dura to be segmented as cortex in some areas?
Bruce Fischl wrote:
you can use mri_info on your dicoms to find out the resolution. Hopefully it's not too far from 1mm isotropic. If it's 1.5 or bigger in any dimension that might explain the trouble.
On Tue, 6 Nov 2007, Watson, Christopher wrote:
The acquisitions are SPGRs, taken on either a GE 3T or 1.5T (I'm not exactly sure, I'm new to the job). Yea, in a lot of areas the dura is adjacent to the grey matter. Those are certainly the problem areas - in most other areas the segmentation is excellent. I'm not sure of the resolution.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 11/6/2007 8:49 PM To: Watson, Christopher Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz
Hi Chris,
what type of acquisition are you using? Dura can be really hard to deal with, as it can look just like gm, depending on your MR parameters, and it is can also be physically adjacent to gm. That said, it's only usually a problem in localized areas. What resolution is your data? We have some newer sequences and code that avoid the dura, but they are by no means standard (and we only have them for Siemens).
cheers, Bruce
On Tue, 6 Nov 2007, Chris Watson wrote:
Hello all, I was wondering if there is a quick way to make edits to multiple slices of the aseg.mgz (or the brainmask.mgz) volume.
Specifically, I am working on my first subject, and it seems that on almost every slice, pieces of the dura/skull/arachnoid/what-have-you get segmented as cortex (less often, pieces of dura are included within the boundary of the pial surface). I've worked on some slices by manually removing/de-segmenting the pixels that need to go, but this is proving to be extraordinarily time-consuming (some of the slices I've worked on can take 10 minutes easily; perhaps I am obsessing too much, but am trying to get it as close to perfect as it should look). For over 100 slices, even 5 minutes/slice of editing will take several hours. I tried changing the mri_watershed parameter on another subject, but that didn't seem to fix anything.
Any tips to save me hours will be greatly appreciated.
-Chris _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer