The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia
2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Hi Claudia > > can you describe the problems? And cc the list so that others can help? > thanks > > Bruce > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? >> >> I'm trying to upload data, but I've problems with your server. >> Cheers, >> Claudia >> >> >> 2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Hi Claudia >> >> it really depends on the individual case and what's causing the >> exclusion. Does the wm.mgz look accurate? If so, you may have a >> topological defect that is being fixed incorrectly. Usually we >> focus on fixing the white boundary and that will also correct >> the pial. You can set the expected gray matter intensities in >> the xopts file, but that is rarely necessary and only if your >> gray matter looks very different than the sequences we are used >> to. >> >> If you can't sort it out feel free to upload you data. >> >> cheers >> Bruce >> >> >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> Hi Freesurfers,I have a question about pial editing. >> I have some reconructions in which there's a lot of >> grey matter excluded, >> and consequently white metter too. I did correct >> these images manually by >> control points editing, and then autorecon2-cp >> autorecon3, but some cortical >> grey matter continues to not be included in the pial >> surface, and I have >> white matter areas that are still not included in >> either the pial or white >> matter boundaries. >> Is there anyother ethods for adding grey matter in >> the pial surfeces other >> than editing control points (such as by editing >> voxels to add grey matter), >> or something like that? >> Thanks for your help. >> Claudia >> >> >> >> >> 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<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. >> >> >> >>
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