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 <fis...@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 > >> > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- ******************************* 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 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************
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