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SPM  September 2007

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Subject:

Re: Rat fMRI data analysis in SPM - please help!

From:

Volkmar Glauche <[log in to unmask]>

Reply-To:

Volkmar Glauche <[log in to unmask]>

Date:

Fri, 28 Sep 2007 13:19:15 +0200

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (41 lines)

Dear Sak,

On Thu, 27 Sep 2007, SAKTHIVEL SEKAR wrote:

>              I'm working on rat fMRI and looking to get our data 
> analyzed in SPM. After several hours of efforts: the issues with the 
> change in the image dimensions and size of the resulting image after 
> running normalization (i.e. changes to the bounding box & voxel size 
> respectively) was fixed. We understand that this is because of the fact 
> that the default values of the processes in SPM are meant for human 
> brain analysis.

Yes, there are a number of places where implicit/explicit assumptions are 
made about head sizes and image resolutions. This includes sampling 
distances for spatial registration (realign, coregister, segment, 
normalise), affine regulation for normalisation, bounding box for writing 
normalised images. Most of these can be changed without too much effort.
What can't be changed easily is spm_orthviews display - in "Full volume" 
zoom mode spatial resolution is limited to 1mm. For animal data, this 
usually means you have to zoom in to get all voxels displayed.


>              Yet still the issue with the shift in the origin of the
>              resulting data remains unsolved. when compared to the input
>              image the resulting image (after normalization) looks
>              dragged towards a corner and not-satisfactory.

You should make sure that your images are in rough register with your 
templates before normalisation already. Use CheckReg to display a raw 
image and your template, then do "Reorient Image" from the context menu of 
the raw image.

Volkmar

-- 
Volkmar Glauche
-
Department of Neurology		[log in to unmask]
Universitaetsklinikum Freiburg	Phone	49(0)761-270-5331
Breisacher Str. 64		Fax	49(0)761-270-5416
79106 Freiburg			http://fbi.uniklinik-freiburg.de/

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