Also re-sending my query - perhaps someone has experience with contrast adjustments

We have been doing contrast correction using mri_nu_correct.mni after autorecon-all

(e.g.,

mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o FS090620ll/mri/orig/nu2.mgz --n 2).

My question is whether after doing subsequent edits and corrections (such as adding control points, or editing white matter) do we need to specify nu2.mgz as the target file for the recon fix steps in the command line

(e.g.,

recon-all -autorecon2-cp -autorecon3 -s FS090620ll -i FS090620ll/mri/orig/nu2.mgz -force)

thanks
ilana

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Ilana Hairston ,PhD
Research Assistant Professor
4250 Plymouth Rd. (rm 2439)
Psychiatry Department, Addiction Research Center
University of Michigan, Ann Arbor MI 48109-2700
Tel: 734-232-0232; Mobile: 650-906-8449
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Sentimental Insomnia and Nostalgia Disorders Sciences

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