I think it is because n3 sometimes creates a few voxels that are very bright (or can't handle a very bright voxel that is there), then the conform step ends up compressing a lot of voxels into the dark range to handle the few bright voxels. I put some stuff in recon-all to try to reduce the effect.
doug On 08/08/2013 11:46 AM, Bruce Fischl wrote: > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
