maybe try scaling up the orig.mgz then? I never really understood why the nu darkens it sometime. Alternatively you could scale up the nu, but you will have already lost dynamic range
On Thu, 8 Aug 2013, aqure...@nmr.mgh.harvard.edu wrote: > The 001.mgz actually looks good in this case (in terms of intensity) so > I'm not sure if it makes sense to scale it up further. The problem is with > the nu.mgz being too dark. I'll try it out though if you think it will > also work in this case. > > - Abid > > > --------------- > > you could try using --scale <scale factor> to scale the intensities of the > 001.mgz up > > --------------- > >> Hi Dr. Fischl, >> >> I had a couple subjects that failed recon-all. Although the error log said >> recon-all failed at mri_watershed it looks like the root problem is a >> couple steps earlier, because the nu.mgz looks too dark. This was >> discussed in a previous thread from 2008. >> >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. >> >> You wrote, "p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes >> nu_correct can create very dark images, and there are some switches you >> can loo through to correct them. Alternatively if it is the 001.mgz, >> mri_convert has a scale option you can use." >> >> On my subject 001.mgz looks good (there was no 002.mgz file). It is only >> nu.mgz that looks too dark. It looks like the solution you gave then was >> for a problematic 001.mgz file, but from your response it looks as if the >> problem was nu.mgz the solution would be different. What are the switches >> you can loop through to correct the nu.mgz. >> >> Thanks, >> Abid >> >> > > > _______________________________________________ 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.
