that's what I thought, but it's the orig, not the nu. I think it's the histogram in mri_convert. The mdeft looks like it has a lot of very bright vessels in it, maybe more than we ignore
On Fri, 18 Jun 2010, Douglas N Greve wrote:
This might be a problem with the way we call nu_correct. I had a similar problem a few months ago. I changed mri_nu_correct.mni, and the problem went away, so you may need the new version (attached). Make sure to make a backup.
doug
Bruce Fischl wrote:
Hi Frank, is it the orig.mgz that is dark, or the nu?
cheers Bruce
On Fri, 18 Jun 2010, Frank Scharnowski wrote:
Dear Freesurfers,
When importing a 3T MDEFT structural scan into freesurfer with 'mri_convert subjectname.nii 001.mgz', the image looks extremely dark (see attached tkmedit snapshot). The results of recon all are suboptimal, probably due to the bad intensity normalization. In SPM the structural looks just fine. Is there a way to correct for this?
Many thanks for your help, frank
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