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
|