Dear all,
I am trying to write a script that transforms a set of world space
coordinates (x,y,z) from a native space image to the MNI space
counterparts (x', y', z'), based on the normalization parameters in the
*_seg_inv_sn.mat files.
We use unified segmentation to normalize our images, as it also produces
the inverse normalization parameters.
I understood I have to use the inverse normalization deformation fields
based on the DCT parameters and affine matrix stored in this matfile, as
explained here:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0702&L=SPM&P=R47018&I=-3
and here:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind06&L=SPM&P=R782514&I=-3&m
=23342
But when I write out the deformation maps using
'TASKS>Util>Deformations', I get a 5D nifti file (?? 4th dimension is
1), where I can only access one image in spm (or when using
spm_vol/spm_read_vols).
In short:
- could someone explain to me how exactly I can use these deformation
vector fields to map a point (x,y,z) from individual native space to MNI
space, based on the *_seg_inv_sn.mat file produced during segmentation
in SPM5?
- how can I extract a certain volume from from a 5D nifti file?
Many thanks for any pointers, and have a nice weekend!
Bas
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B.01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]
Web : http://www.fmri.nl/people/bas.html
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