Hi
I am having a problem using DARTEL to normalize my functional MRI images. A similar problem was reported back in September 2009 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;43103dd0.0909) but there was no clear resolution.
I have SPM with the latest updates.
I followed the procedures specified in section 41.1.4 of the manual.
Please see attached image- the functionals show the problem (as if the brain was communicating with heaven or a vacuum cleaner). Note that the native functional image as shown in the coregistration does not have any artifact at the top of the head.
Normalization of the gray matter segment is correct (middle image) and coregistration of the mean functional with a scalped version of the T1 is good.
Here is a list of my preprocessing steps.
1) realign functionals and create a mean image and reslice functionals
2) slice time correct functionals
3) coregister mean functional (source) to T1 (reference) with functionals as other images. I tried this with both the standard T1 and a skull stripped T1 with no difference in problem.
4) segment the T1 using the New segment toolbox.
5) Dartel: create template using rc1 and rc2 images.
6) Dartel: normalise to MNI. Few Subjects. I select the flow field for that subject and the functional images. voxel size-[3 3 3].
The result is shown in the image.
Any idea why this is happening and how to prevent it? Can the functionals be masked in some way to prevent this?
Thank you,
Darren
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