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Subject:

Re: DARTEL - voxel normalisation

From:

Joao Pereira <[log in to unmask]>

Reply-To:

Joao Pereira <[log in to unmask]>

Date:

Wed, 8 Oct 2008 19:42:57 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (129 lines)

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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