I am working with DARTEL to normalize some fMRI data. In some resulting images, there is distortions in the data, such as what is  shown. The data does not have whole brain coverage, and based on previous posts it looks like this is not really a problem, as DARTEL  is pulling data to where there is none, but the data in the voxels in which there is actually EPI data are not affected by this. Thus, as  long as I make sure these voxels are not included in the final   statistical analysis, we should be OK.

But I want to confirm that is true. In both ofo the attached images, the 'pulling' distortion corresponds to regions without whole brain
coverage.

It also happens to be the case that this seems mainly present in the brains of older participants (we have young and old, and the older  people seem to have greater distortion in general.

Lastly, I'll post my work flow, to make sure there are no issues here.

1. The EPI data is slice time corrected and unwarped using field maps.

2. The anatomical images are reoriented manually, as the origin in  most scans is in the splenium of the corpus callosum. When I select
reorient, I apply this reorientation to the ua*.nii EPI files. I do  this after the unwapring because I need to keep the field maps in
regeister with the EPI scans and prefer to avoid potential  registration issues.

4. coreg the EPI (ua*.nii) to the T1. Looks good.

3. Segment the T1 scans, DARTEL outputs for c1 and c2 (grey and white matter).

4. Run spm_dartel_template with default parameters, calling the rc1  and rc2 files.

5. Run normalize using Template 6 and the ua*.nii EPI files.

I have been trying to improve the normalization for several days, and  nothing seems to substantially reduce the distortion I see in the  attached image. I'd appreciate any insight into what I should do (e.g.  ignore it, change parameters, use an alternate normalize option, etc).

Colin Hawco, PhD
Neuranalysis Consulting
Neuroimaging analysis and consultation
www.neuranalysis.com
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