Hi Abid what version of FS are you using? Bruce On Wed, 7 Aug 2013, aqure...@nmr.mgh.harvard.edu wrote:
> 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 > > > _______________________________________________ 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.
