Actually it could not be WM, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that?
2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > visually is the only way. Do you think it is white matter? > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > Yes it's my doubt too, but how can I check this? >> >> >> 2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> then it's not rerunning the -cp. And is it really wm if it's >> that dark? >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> Bruce,no the intensity is lesser then 110 at those voxels, >> it's like 60-70. >> Claudia >> >> >> 2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> is the intensity at those voxels 110 after you have >> processed >> with autorecon2-cp? >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> 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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