The scrips I sent to the list do:
Normalize -> Segment
However, the Normalize step involves matching GM to a GM template, and
therefore involves a segmentation step. This initial segmentation step
requires the prior probability images to be matched to the image for
segmenting, so involves an affine registration.
I guess the procedure could be represented by:
Normalize (affine - to a T1 template) -> Segment
-> Normalize (nonlinear - to a GM template) -> Segment
Its a bit circular, but is a pragmatic solution that works reasonably well.
I think the ideal solution would be some kind of EM algorithm that alternated
between segmenting, bias correcting and warping. I started working on this,
but I have a long way to go. Simple iteration of the current implementations
does not converge to a good solution (which would indicate that there is
room for improvement somewhere).
Best regards,
-John
> > One more question. I'm not so good with matlab code and I had a question
> about the second script.
> I can't tell just by looking at the code which of the following scenarios
> it's doing:
>
> A) Normalize -> Segment
>
> B) Normalize -> Segment -> normalize (to tissue specific template)
>
> Or
>
> C) Segment -> Normalize (to tissue specific template ?)
> > I am looking to reanalayze a good chunk of my data using the Good method
> > and spm2b.
> > 1. I've found a couple different scripts. My understanding is that Script
>
> 1
>
> > is to get modulated images while script 2 is for unmodulated. But both
> > can be used in spm2b. correct?
> >
> > Script1:
> >
> >
> > VN = spm_write_sn(V(i),prm,dnrm.write);
> > VT = spm_segment(VN,eye(4),dseg);
> > clear VN
> > VT(1).fname = fullfile(pth,['G' nam ext]);
> > VT(2).fname = fullfile(pth,['W' nam ext]);
> > spm_write_sn(VT(1),prm,'modulate');
> > spm_write_sn(VT(2),prm,'modulate');
> >
> > Script2:
> >
> > VN = spm_write_sn(V(i),prm,dnrm.write);
> > spm_segment(VN,eye(4),dseg);
>
> Script1 creates modulated, segmented and spatially normalised GM and WM
> images,
> whereas Script2 creates segmented and spatially normalised GM, WM and CSF.
>
> > 2. The email I found said the unmodulated data script had not been
> > tested. Does anyone have any first hand experience using it, finding it
> > to be reliable?
>
> I still haven't tested it.
>
> > 3. I read something about images that are in radiological convention
> > needing to be flipped for spm2b? Can you explain that further?
>
> Although SPM2b still uses the Analyze file format, and will therefore
> read image files from previous versions of SPM, there are differences in
> the algorithms, templates and models used in SPM2 over previous releases.
> Therefore, we recommend you use a single SPM version for any given project.
>
> One thing to watch out for is the image orientation. The proper Analyze
> format uses a left-handed co-ordinate system, whereas Talairach uses a
> right-handed one. In SPM99, images were flipped at the spatial
> normalisation stage (from one co-ordinate system to the other). In SPM2b, a
> different approach is used, so that either a left- or right-handed
> co-ordinate system is used throughout. The SPM2b program is told about the
> handedness that the images are stored with by the spm_flip_analyze_images.m
> function and the defaults.analyze.flip parameter that is specified in the
> spm_defaults.m file. These files are intended to be customised for each
> site.
> If you previously used SPM99 and your images were flipped during
> spatial normalisation, then set defaults.analyze.flip=1. If no flipping
> took place, then set defaults.analyze.flip=0.
>
> Check that when using the Display facility (possibly after specifying some
> rigid-body rotations) that:
>
> * The top-left image is coronal with the top (superior) of the head
> displayed at the top and the left shown on the left. This is as if
> the
> subject is viewed from behind.
> * The bottom-left image is axial with the front (anterior) of the
> head at the top and the left shown on the left. This is as if the subject
> is
> viewed from above.
> * The top-right image is sagittal with the front (anterior) of the
> head
> at the left and the top of the head shown at the top. This is as if
> the
> subject is viewed from the left.
>
> > 4. I'm assuming that the script takes in the T1 reoriented images in
> > analyze format?
>
> Analyze format images should be fine. See "Data Format" in the online help
> [spm_format.man in the distribution].
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
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