Hi Zhi,
> The activation map overlaid on the T1 image very well after the T1 image was
> normalized using the seg_sn.mat file. Thank you!
Glad to be of help.
> The following question is: Must I follow the steps in the SPM5 Manual(Session VI
> Chapter 25) if I want to overlay the activation map overlaid on the same one's T1
> image? Is there any other way to get seg_sn.mat file besides segmenting the T1 image?
There are very few "must" in image processing, and a lot of "can"... as
the name implies, no, there is no other way to get a seg_sn.mat file
besides segmenting. However, as you correctly stated,
> I found that a _sn.mat file would be got after normalize the fMRI
> data(estimate and write, the steps as below). Can I use the _sn.mat file
> to write the T1 image?
The dry answer is yes, but I would think the best way to find this out
is to try it out (and you will see for yourself). The argument against
it is that the T1 has higher spatial resolution and normalization will
thus usually be "better" (whatever that means) if you do it this way around.
> 1. realign the fMRI data
> 2. normalize(estimate and write) the fMRI data: source image is the
> mean image(mean01.img and mean01.hdr) got from the realign step,
> images to write are the realigned fMRI data, the template image is
> the EPI.nii in the SPM5's template directory.
> 3. write the T1 image using the mean01_sn.mat file
Your T1 may look a bit funny when normalized with EPI-based parameters,
and you will still have to coregister the two.
Best,
Marko
--
=====================================================================
Marko Wilke (Dr.med./M.D.)
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Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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