Hi, DARTEL experts,
I'm new in using DARTEL with spm8 to normalize fMRI data to the MNI space. I have used DARTEL for structure (T1 images) segmentation and normalization before, but not with EPI images. I have read the DARTEL guide in SPM8 manual and related messages in the spm message archives, but still not clear about the specific steps. Here are my questions.
1. Do I need to segment and normalize multiple subjects' TI images first to create the template and flow field images in order to normalize a subject's EPI images? Can I run the segmentation and normalization with one subject's T1 and EPI images only? If the latter is possible, how to set up the steps using DARTEL? (Single subject analysis is desirable if I want to look at the data before other subjects' data are acquired.)
2. If the structure segmentation and normalization must be done with more than one subject's images, is the coregistration between the subject's T1 and EPI images necessary?
3. Once the T1 segmentation and normalization are completed, how to apply the normalization parameters to the EPI images (already realigned and resliced)?
4. A slightly different but related question: I have segmented (using New Segment with the default settings) and normalized (using preserve "amount") two subjects' TI images (mprage, voxel size = 1x1x1). However, the c1 images clearly included part of the non-gray matter tissues on the top and the posterior part of the brain (see the attached image file "DARTEL New Segment"). These non-gray matter tissues also seemed to be carried over to the template images (attached "DARTEL smwc1"). What parameter settings I should try that may improve the segmentation step?
5. I also realized that in creating the "template," DARTEL requires all T1 images to have the same number of slices. All my T1 images have the same voxel size, but some subjects' images have a few more slices than others although the brain and the top of the skull are covered in all subjects even without the extra slices. Is there a way to have DARTEL accept images with different number of slices?
Thank you very much for your help.
Ben
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Benjamin Xu, Ph.D.
7D51 Bldg 10 Center Dr.
Human Cortical Physiology Section/NINDS
The National Institutes of Health
Bethesda, MD 20892
Tel: 301-402-7968
Fax: 301-480-2286
Email: [log in to unmask]
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