Problem of normalization in processing of mouse fMRI data

Submitted by liq2005liq on Mon, 11/10/2014 - 20:31

Hi, Chao-gan

I recently use SPM to process the resting-state fMRI data of mice. I met a problem when I tried to normalize the fMRI data. I used the default parameters set in SPM8 and I found that the results of normalization is like what showed in the attached picture. A large part of the brain was cut.  It seems that the origin in not right.  Do you think so? I used MATLAB to convert the format of Bruker raw images into NII images. The parameters of the nii images are showed in the following mricro picture(attached). The origin of the nii images is x=2,y=2,z=2 by default.  I don't know how to change the origin into ideal or right origin same with that of human.  Can you give me some advice? Thank you very much!

Best

Qiang

 

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Image icon problem of normalization47.63 KB
Image icon nii parameters143.57 KB

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YAN Chao-Gan

Mon, 11/24/2014 - 19:31

I think the key thing is that you have to find a correct mouse template.

Best,

Chao-Gan

liq2005liq

Thu, 12/18/2014 - 05:06

Hi, Chao-gan

Thank you for the advice. 

Best

Qiang