I forgot about this. The procedure needs another step, which can be achieved
in one of two ways:
5.1. Using Deformations -> Composition
5.1.1 Inverse -> Composition -> Imported _sn.mat -> chose template 6 and
base inverse on native space scan of each subject
5.1.2 DARTEL flow -> u_rc1* files for each subject + *"Forward"*
5.1.2 Identity, with the image to base it on being the
original scan.
This is similar to the steps described in Section 1.4 of the DARTEL guide,
except that the mapping from Template_6 to MNI space is from the inverse of
the transform contained in the _sn.mat, rather than a DARTEL deformation.
The other way would be to use the matrix information in the headers, but I
won't elaborate on this.
Best regards,
-John
On Wednesday 08 October 2008 19:42, Joao Pereira wrote:
> Dear John,
>
> Thank you very much for your reply. Just one more thing:
>
> When I try to apply these steps in the reverse order you suggested, the
> output y* file has 91x109x91 dimensions, whereas I need the original
> dimensions for it to be usable. Should then 5.1.2 be:
>
> Inverse -> Composition -> DARTEL flow -> u_rc1* files + (and now I get lost
> given I already have an inverse) Backwards/Forward? + native space image to
> use as basis for inverse
>
> Please let me know if this is correct.
>
> Thank you once again!
>
> Joao
>
> -----Original Message-----
> From: John Ashburner [mailto:[log in to unmask]]
> Sent: 08 October 2008 16:07
> To: Joao Pereira; [log in to unmask]
> Subject: Re: [SPM] DARTEL - voxel normalisation
>
>
> Section 1.2.2 of the DARTEL guide describes how to generate a mapping from
> MNI
> space to Template_6.nii to individual subject. What you are after is the
> inverse of this, which is a mapping from individual subject to
> Template_6.nii
> to MNI space. You therefore need to swap some of the operations around:
>
> 5.1. Using Deformations -> Composition
> 5.1.1 Inverse -> Composition -> Imported _sn.mat -> chose template 6 and
> base inverse on native space scan of each subject
> 5.1.2 DARTEL flow -> u_rc1* files for each subject + *"Forward"*
>
> The rest seems fine. This stuff can be a bit tricky to get your head
> around -
> but it gets easier with practice.
>
> Best regards,
> -John
>
> On Wednesday 08 October 2008 14:33, Joao Pereira wrote:
> > Hello,
> >
> > I've been trying to extract the normalised positions (after DARTEL) of
> > points placed in native space.
> >
> > I've come up with a methodology for this purpose (for each cohort) which
> > I would like you to comment on if possible:
> >
> > 1. Normalise all scans and extract mwc* files, as well as the *seg_sn.mat
> > file for each scan
> > 2. DARTEL Tools -> Initial import, using all seg_sn files and setting
>
> voxel
>
> > size at NaN
> > 3. Create Template using rc1* and rc2* files
> > 4. Affine transform the DARTEL template (#6) to MNI and extract the
>
> *sn.mat
>
> > file (I need my coordinates in MNI)
> > -- (New bit starts here) --
> > 5. Estimate the deformation field from initial (native) scan to DARTEL
> > output by:
> > 5.1. Using Deformations -> Composition
> > 5.1.1 DARTEL flow -> u_rc1* files for each subject + *"Forward"*
> > 5.1.2 Inverse -> Composition -> Imported _sn.mat -> chose template 6
> > and base inverse on native space scan of each subject
> > 6. Use y_* output to locate normalised position of native point (x,y,z)
> > by using f = nifti(y_*); norm_pos = squeeze(f.dat(x,y,z,:,:));
> >
> > Please let me know if this is sensible. Thank you all very much for your
> > help!
> >
> > Best,
> >
> > Joao Pereira
> >
> > -----Original Message-----
> > From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On
> > Behalf Of John Ashburner
> > Sent: 08 October 2008 13:39
> > To: [log in to unmask]
> > Subject: Re: [SPM] DARTEL: import image segmentations
> >
> >
> > The cleanup procedure is something that I cobbled together one afternoon
> > and kind of works in a bit of an ad hoc way. I was therefore reluctant
> > to make it the default behaviour for DARTEL import (in the hope of
> > replacing it with a proper MRF type approach). For the data here in the
> > FIL, this option doesn't make so much difference - but it may make help
> > for data
>
> from
>
> > other groups. If this is the case for the DRG scans, then I would
> > suggest uncommenting this line.
> >
> > All the best,
> > -John
> >
> > On Wednesday 08 October 2008 10:53, Rachael Scahilll wrote:
> > > Dear John
> > >
> > > I have imported some images ready to create a template using DARTEL and
> > > found that some of the segmentations contain a lot of non-brain tissue.
> > > When performing the initial segmentations to generate the normalisation
> > > parameters I used the 'thorough clean' option which greatly improved
> > > the segmentations.
> > >
> > > Line 121 in spm5/toolbox/DARTEL/spm_dartel_import.m:
> > > [dat{1},dat{2},dat{3}] = clean_gwc(dat{1},dat{2},dat{3}, 2);
> > > appears to be commented out. Just wondered if it was possible to put
>
> that
>
> > > option back in or is there a good reason why this is not an option when
> > > generating the rigidly-aligned segmentations for template creation?
> > >
> > > Thanks,
> > >
> > > Rachael
> > >
> > >
> > >
> > > Dr Rachael Scahill
> > > Senior Imaging Research Associate, Track-HD
> > > Institute of Neurology
> > > Box 104 Queen Square
> > > London WC1N 3BG
> > > UK
> > > +44 (0)20 7905 2990
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