[VoxBo] normalization using SPM procedures

[Joonkoo Park]

Thanks a lot!
Two more following questions:

I normalized my functional image(s) [dimension 64*64*30] using EPI.nii 
template [dimension 91*109*91] in SPM5. But then the normalized image 
has a dimension of 79*95*69, when my common sense expects the dimension 
of the normalized data to be the same as the template. And in fact some 
edges of the brain are cut off. Would this be something normal?

I also noticed that if I want to normalize a .tes file with 150 time 
points, then I first convert .tes into 150 different .img files and 
transfer them to SPM, then normalize, then possibly convert them back 
into a .tes file. Would this be a normal procedure? It seems like a LOT 
of grunt work (for all runs of every subject), and thought there's 
gotta be a way around it.

I've looked into SPM manuals for these issues but couldn't find a good 
explanation. Thanks in advance. JP




Quoting Charan Ranganath <cranganath at ucdavis.edu>:

> Hi, I think I can suggest two potential solutions:
> (1) Take the t1.nii image and skull strip it using the brain 
> extraction tool (BET). The program is described at: 
> http://www.fmrib.ox.ac.uk/analysis/research/bet/
>
> (2) Normalize your EPIs to the EPI template included in SPM.
>
> We have found that we get better across-participant registration with 
> approach #2. However, if your EPIs have a lot of dropout and 
> distortion or if they only cover part of the brain, you will have to 
> use #1.
>
> Good luck. CR
>
> Joonkoo Park wrote:
>> Hello,
>>
>> As recommended by VoxBo wiki, I'm trying to normalize images using SPM5.
>> I first convert the (anatomical) .cub files into .hdr and .img 
>> (using vb2img) and use SPM procedures to calculate *_sn.mat and 
>> eventually warp the original .img image to a normalized one. I used 
>> T1.nii file in spm/template folder as a template for calculating 
>> parameters for anatomical images.
>>
>> One problem I see here (well, it would be the same case if I were to 
>> use VoxBo norm) is that my anatomical images (i guess functional 
>> images too) do not include skull, but the template includes skull 
>> and other parts of the head. I am worried that my anatomical image 
>> will assume that even the skull part of the template is part of the 
>> brain, and this seems to the case when I look at the normalized 
>> images.
>>
>> The skull part of my images are eliminated during the preprocessing 
>> procedure at the scanner site. Is there a way to solve this problem?
>>
>> Thanks!
>>
>
> -- 
> Charan Ranganath, Ph.D.
> Associate Professor
> Center for Neuroscience and Dept. of Psychology
> University of California at Davis
> 1544 Newton Ct.
> Davis, CA 95616
>
> phone: 530-757-8750
> fax: 530-757-8640
>
> http://DynamicMemoryLab.org
>
>
>
>