sorry for being dense - but what then would be the best way to acheive better wm intensity? We get much better contrasts and better segmentation in fronto-temporal regions when we run mri_nu_correct.mni. But then we still need to fix topological errors. My understanding is that '-make all' fixes or finishes up an incomplete recon, will it incorporate control points or white matter edits (we're running 4.5 so it should work)?
Alternatively - Is there a way to add the contrast correction as a flag during autorecon-all from the start? (seems the most logical)
thanks ilana
On 4 May 2010 17:01, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ilana
that won't work. I guess you could try copying nu2.mgz to nu.mgz and trying -make all (assuming you have a new enough version of recon-all)
cheers Bruce On Tue, 4 May 2010, Ilana Hairston wrote:
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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