Here are some snapshots of my T1 and T2 images, and my results after
running new segment with 6 tissue classes and again with 3 tissue
When I use the default TPMs (spm8/toolbox/Seg/tpm.nii), which uses 6
tissues as far as I understand, I get what I have attached as the 6class
images, but actually I get 9 of them - C1, C2, C3, C4, C5, C7, C8, C9,
C10. C1 and C7 both appear to be versions of white matter, but at
different ends of the spectrum. C2 and C8 seem to both be WM, but again
neither one is complete on its own. C3 and C9 are CSF, and the rest
composed of are edge voxels, which I assume represents what new segment
decided was bone and soft tissue.
When I use only the first 3 classes (removing tissue maps 4, 5 and 5) I
get the results labeled as 3class images C1, C2, and C3, which seem to
be pretty good GM, WM and CSF images.
So, I guess I am concerned that with the 6 classes I am getting two
separate GM images, neither of which is complete on its own, and I would
think I should only use one. Am I making an assumption that isn't
correct? Or does DARTEL know how to handle this correctly, and I should
just move on...
From: John Ashburner [mailto:[log in to unmask]]
Sent: Thursday, July 09, 2009 3:44 PM
To: Pierson, Ronald K
Cc: [log in to unmask]
Subject: Re: [SPM] New Segment on T1 and T2, brain-only images
You should be able to run the new segmentation on the skull-stripped
data without any tweeks, providing the stripped off voxels are set to
either 0 or NaN. Values of 0 or NaN in the image will be ignored.
On Thu, 2009-07-09 at 18:37 +0100, Ronald Pierson wrote:
> I want to preprocess some scans for VBM using new segment and DARTEL.
> I want to use both T1 and T2 scans, and they are currently
> brain-clipped. In new segment can I run it with just the first three
> tissue classes, since there are no non-brain tissues present? Any
> other suggestions, or is there a tutorial/procedure manual available
that would be useful for me to look at?
> Ronald Pierson
> Chair of Imaging, PREDICT-HD
> Manager, Research and Development
> Department of Psychiatry, Carver College of Medicine
> W-278 GH, 200 Hawkins Dr
> Iowa City, IA 52242
John Ashburner <[log in to unmask]>