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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