I'm uploading my subjdir on FTP server. Thanks a lot. Claudia
2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Hi Claudia > > if you upload your whole subject and send us some example voxel coords of > where you are looking we will take a look > > Bruce > > > On Mon, 29 Apr 2013, Claudia Dacquino wrote: > > I'm sorry Bruce I'm confusing you.The fact is that those areas are >> labelled >> >> as WM, so I thought those were white matter, but looking with more >> attention >> at wm.mgz I did realize that they could me no WM, as you seggested me, >> because they are too dark. >> I'm new and I'm learning by trial and error. >> Cheers, >> Claudia >> >> >> 2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Hi Claudia >> >> now I'm confused. Did you put control points in those voxels? >> You definitely, definitely must avoid putting them in voxels >> that contain anything other than WM. The pial surface will >> usually be incorrect if the white surface is incorrect, so the >> first thing to do is make sure it is right >> >> Bruce >> >> >> On Mon, 29 Apr 2013, Claudia Dacquino wrote: >> >> But in "brainmask.mgz lh.white -aux T1.mgz >> -aux-surface rh.white >> -segmentation aseg.mgz" it's labeled as white >> matter, could it be possible? >> >> >> 2013/4/29 Claudia Dacquino >> <claudia.dacqu...@gmail.com> >> 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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