For New Segment I believe you have to write out the deformation fields instead. Then you can write out the new images using the Deformations utility.
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From: SPM (Statistical Parametric Mapping) [[log in to unmask]] On Behalf Of Courtney Brown [[log in to unmask]]
Sent: Thursday, October 28, 2010 11:58 AM
To: [log in to unmask]
Subject: Re: [SPM] SPM8 Segmentation Issue

Thank you for the helpful responses to my post. I have run my images through SPM8 "New Segment," which does indeed improve the quality of the segmented images considerably. I am attempting to continue the pre-processing of these images (specifically, Normalize and Smooth the fMRI images) and am running into a problem: the normalization parameters produced by "New Segment" (seg8.mat) is not recognized as a parameter file for the Normalize and Write step (error code generated pasted below):

Running 'Normalise: Write'
Failed  'Normalise: Write'
Reference to non-existent field 'VG'.
In file "/usr/local/share/data/spm/spm8/spm_write_sn.m" (v2534), function "get_xyzmat" at line 430.
In file "/usr/local/share/data/spm/spm8/spm_write_sn.m" (v2534), function "spm_write_sn" at line 96.
In file "/usr/local/share/data/spm/spm8/config/spm_run_normalise_write.m" (v2312), function "spm_run_normalise_write" at line 25.

Running 'Smooth'
Done    'Smooth'
The following modules did not run:
Failed: Normalise: Write

My question is: Is there a way to generate a seg_sn.mat file that would be compatible with the Normalize and Write step? Alternatively, is there a more appropriate way to normalize and smooth fMRI images using the parameter file generated from "New Segment?"

Thank you in advance,

Courtney Brown


On Mon, Oct 25, 2010 at 8:17 AM, John Ashburner <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Both of these segmentation failures are due to poor initial affine
registration.  Essentially, if the initial alignment with the tissue
probability maps is not so good (maybe because of intensity
nonuniformities, large initial misregistrations, or incorrect voxel
sizes etc) then the kinds of results we see here may be expected.  The
algorithm behind the Segment button does not include any knowledge of
what would be expected outside the brain, as the tissue probability
maps are only of GM, WM and CSF.  One of the effects of this is that
the initial affine registration may be less robust.

If you use SPM8, there is an alternative segmentation routine
available from among the toolboxes (with the unimaginative name of
"New Segment").  This implementation includes some additional
knowledge of non-brain tissues, so is generally more robust.  It will
eventually become the default segmentation routine, but only after I
have written some more code to use the deformation fields it produces
for spatial normalisation.

Best regards,
-John

On 23 October 2010 16:10, Courtney Brown <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Hello,
>
> I am having some difficulty with the segmentation step within SPM8. I am
> looking at healthy young adults completing fMRI paradigms. After outputting
> grey matter and white matter segmented files from the anatomical image, I
> have gotten strange results (please see attached jpeg images). This does not
> happen each time I run segmentation, but I have gotten similar output files
> on several occasions. I have tried running segmentation with the cropped
> anatomical image as opposed to the original anatomical image. The images
> above involve the SPM8 segmentation default settings. I have also tried to
> adjust some of the segmentation defaults (higher/ lower Bias regularisation,
> higher/ lower Bias FWHM), but have gotten similar results in each case.
>
> My question is: Does anyone have a sense of what would cause these types of
> images being outputted after the segmentation step. And furthermore, what
> would be the best resolution to this issue in order to adequately preprocess
> fMRI images for analysis?
>
> Any input would be greatly appreciated.
>
> Thank you,
>
> Courtney Brown
>
> Graduate Student
> Department of Psychology
> University of Georgia