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.
