Hi Jeff,
sorry, I don't know what causes the nu_correct to do this, but you'll probably have to skip that step as otherwise you've lost too much dynamic range. I would try copying orig.mgz to nu.mgz and running all the steps afterwards.
cheers Bruce On Wed, 7 Oct 2009, Jeff Sadino wrote:
Hello,
I asked this question a couple days ago, but never got an answer. Please excuse the double posting. I am running FS 3 and am having problems with auto-recon1, in particular the mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my nu.mgz image has intensities all below 20. I am having errors further down the line, but I think they are all due to this step. Can anyone help me get my intensity values to work out right?
Thank you! Jeff Sadino