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I have no idea what has happened here.  Unless the number of tissue
classes is changed, there should be only six classes (c*.nii) qritten
out at the most.  Could you email me the batch job so I can take a look?

Alternatively, it could be a bug that I have not yet experienced.

Best regards,
-John

On Thu, 2009-07-09 at 16:12 -0500, Pierson, Ronald K wrote:
> Here are some snapshots of my T1 T2 images, and my results after going
> with both 6 tissue classes and 3 tissue classes.
> 
> When I use the default TPMs (spm8/toolbox/Seg/tpm.nii), which uses 6
> tissues as far as I understand, I get the 6class images, but 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 are edge voxels.
> 
> When I use only the first 3 classes I get the 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...
> 
> Ron
> 
> 
> 
> -----Original Message-----
> 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.
> 
> Best regards,
> -John
> 
> 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]>