Hi Luis,
let me try (and add that I may fail as I am not sure what exactly you
want, but let's see):
> I'm new with SPM and I don't know how to convert the tissue probability
> maps obtained by “Segment” into functional space.
One thing that may add to my confusion is that the term "tissue
probability maps" is usually reserved to the tissue priors used by the
segmentation algorithm. The individual results would be the tissue class
images.
> 1) Realign: estimate&write of functional images → I obtained rfunctional
OK (although it is not necessary to write out the images here, you
should use "estimate only" and save one interpolation step).
> 2) Coregister: estimate Reference:anatomical, source:
> meanfunctional, other images: all the rfunctional
OK (now your functionals and your anatomical are in the same [native]
space).
> 3) Segment: data: anatomical Tissues: TPM priors option: native
> space → I obtain the corresponding c1 c2 c3
OK.
> 4) Normalise write: deformation field: y_anatomical.nii, data: all the
> rfunctional images.
OK (although you might simply do your statistics in native space and
only normalize the parameter maps, i.e., the con-images and do your
second level analyses on these).
> I need the tissue probability maps (TPMs) from step 3 in functional
> space, how can I transform them?
As I said, the TPMs are usually the reference tissue maps; if this is
what you mean, you will have to use the inverse of the normalization
field and apply it to the priors. See the archives for several mails on
this. If you want normalized individual tissue maps, you simply write
out the results as, say, unmodulated normalized wc1, wc2,... images.
> Furthermore, I don't know how to
> extract the transformation matrix from the coregistration step
> (functional to anatomical).
I don't think this is easily done via the batch but you can use
something like
x = spm_coreg(reference_image,image_to_be_moved);
M = inv(spm_matrix(x));
If you then want to apply it to an image, do
MM = spm_get_space(image_to_be_moved);
spm_get_space(image_to_be_moved, M*MM);
> Thank you very much,
You're welcome.
Cheers,
Marko
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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