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[log in to unmask]" type="cite">Pieter,

If you only need it once, you can apply it to all. When looking in SPM's matlabbatch interface, it does not look like you can implement it there, but you can certainly script it if you hack cg_set_com to accept command line input.

Cheers,
Marko

Pieter Vandemaele wrote:

Hi Marko,

This is excellent. Can this be executed using matlabbatch?

Pieter

Op 29/01/2013 12:00, Marko Wilke schreef:

Hi Pieter,

so your global orientation looks ok, but your origin seems off. The
quickest way to correct this (in my humble opinion) is the option
within vbm8 to reset the origin using the center of mass of the
largest cluster. Works for me and is (hear, hear :) completely
automated. Select vbm8, Extended tools, Set origin using center of mass.

Good luck,
Marko

Pieter Vandemaele wrote:

Thanks for the feedback.
The screenshots were taken with MRICRON.
This is the result with CheckReg in spm.


I did not check out all anatomicals, but it would be a huge burden to
adjust all subjects manually.
I normalised the same data with the Normalisation module and did not
have to reorient the images. Normalisation with the Segment module
fails.
Do you have suggestions to do this fast?
Thx

Pieter

Op 29/01/2013 11:38, Marko Wilke schreef:

Pieter,

I would expect that they are all looking into the wrong direction :)
but I suggest using spm to check that. If you first call up one of the
templates coming with spm, and then your image, they should look
similar with regard to their overall orientation. If not so, you can
use the pitch, roll, yaw fields to enter multiples (or halves) of pi
to reorient your image. Once you're happy with the result, you can
apply the transformation to all your images, using "reorient images".
This changes the header, so you may want to make sure you have backups
first.

Cheers,
Marko



Pieter Vandemaele wrote:

Dear SPM'ers,

I used the Segment module to segment and normalize anatomical scans
and
got strange results, see attachments.
Is this due to the origin localisation?
What is the easiest way to deal with this? I have 80 subjects so a
(semi)automatic solution would be ideal.

Best

Pieter

--
Re: Netwerk MR afdeling UZGent

*Pieter Vandemaele, *MSc-Ing
*GIfMI Site Manager*
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM

[log in to unmask] <mailto:[log in to unmask]>
tel: +32
(0)9 332 48 20
http://gifmi.ugent.be     fax: +32 (0)9 332 49 69

--
Re: Netwerk MR afdeling UZGent

*Pieter Vandemaele, *MSc-Ing
*GIfMI Site Manager*
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM

[log in to unmask] <mailto:[log in to unmask]>     tel: +32
(0)9 332 48 20
http://gifmi.ugent.be     fax: +32 (0)9 332 49 69

--

Pieter Vandemaele, MSc-Ing
GIfMI Site Manager
Ghent Institute for Functional and Metabolic Imaging
MR Department -1K12
Ghent University Hospital
De Pintelaan 185
9000 Ghent - BELGIUM

[log in to unmask]	tel: +32 (0)9 332 48 20
http://gifmi.ugent.be	fax: +32 (0)9 332 49 69