yes. In general you're better of trying to get closer to isotropic voxels
than high in-plane at the cost of thick slices.
Bruce
On Wed, 7 Nov 2007, Chris
Watson wrote:
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:[EMAIL PROTECTED]
Sent: Tue 11/6/2007 8:49 PM
To: Watson, Christopher
Cc: [email protected]
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
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