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Thanks John - I'm now running VBM The New Recipe.

Is it valid, after the initial segmentation, to do a quick-and-easy 
analysis using the c[12]* images, or are they no good?

I'm asking this, because I get weird results doing that. Both the grey 
matter and white matter maps of the same persons seem to show a greater 
tissue volume in follow-up scans than in the initial scans!

 >> n1_1999=nifti('c1f100911_1999.nii');
 >> n1_2009=nifti('c1f100911_2009.nii');
 >> n_1999=n1_1999.dat(:,:,:,:);
 >> n_2009=n1_2009.dat(:,:,:,:);
 >> sum(n_1999(:)).*prod(n1_1999.hdr.pixdim(2:4))
ans =
  7.6070e+05
 >> sum(n_2009(:)).*prod(n1_2009.hdr.pixdim(2:4))
ans =
  7.8465e+05

I'm sure that can't be right, but this is what the segmentations 
suggest. Or is this due to the stretching etc and do we need to wait for 
DARTEL to undo those?

Many thanks
Alle Meije

>
> Subject:
> VBM - segmentation and normalisation
> From:
> John Ashburner <[log in to unmask]>
> Date:
> Tue, 11 May 2010 17:04:52 +0100
>
>
> The DARTEL guide is slightly out of date and was for an older version 
> of the software (and is now removed).  The SPM8 manual contains an 
> updated version for SPM8 (which includes the new segmentation and the 
> option to spatially normalise to MNI space).
>
> People usually want results in MNI space, so the normalise to MNI 
> space option is generally recommended.
>
> Best regards,
> -John
>
>
>     I am doing a VBM-type analysis and trying to set it up using
>     DARTEL. So far with varying degree of success, which is probably
>     due to ignorance..
>
>     Should it be obvious
>
>     1. How to make a batch file for coregistration + segmentation of
>     all the input T1 images?
>     What I did was: make a batch file for coregistration of 1 T1 image
>     to the MNI-space T1 template, and use a dependency to segment the
>     output of the coregistration. The other input image names were put
>     into the same batch file using a script
>     Somewhere along the way, 'new segment' always crashes. With
>     'segment' it is (at least, was) possible to finish this step. Is
>     it equivalent to use 'segment' instead and then do the DARTEL
>     import step separately (instead of having the import step built-in
>     with 'new segment')?
>
>     2. How to normalise the images?
>     In John's DARTEL guide http://www.fil.ion.ucl.ac.uk/~
>     <http://www.fil.ion.ucl.ac.uk/%7Ejohn/misc/dartel_guide.pdf>john/misc/dartel_guide.pdf
>     <http://www.fil.ion.ucl.ac.uk/%7Ejohn/misc/dartel_guide.pdf>, The
>     steps for a group of structural images were
>            1. check reg (or coregister to MNI in my case)
>            2. segment
>            3. DARTEL initial import
>            4. DARTEL create template
>            5. DARTEL create warped
>     But in the VBM tutorial 'notes of the Edinburgh VBM class'
>     http://www.fil.ion.ucl.ac.uk/~
>     <http://www.fil.ion.ucl.ac.uk/%7Ejohn/misc/VBMclass10.pdf>john/misc/VBMclass10.pdf
>     <http://www.fil.ion.ucl.ac.uk/%7Ejohn/misc/VBMclass10.pdf> the
>     procedure is:
>            1. check reg (same)
>            2. new segment (different)
>            3. DARTEL create template (same)
>            4. normalise to MNI (different)
>     One of the differences between 'segment' and 'new segment' is that
>     it creates the files that 'initial import' would otherwise create,
>     so that makes sense.
>     But is it a good idea to normalise to MNI space? Or is it better
>     to warp the images to the DARTEL-created template instead?
>
>
> -- 
> John Ashburner <[log in to unmask] <mailto:[log in to unmask]>>
>