my subjdir is on FTP server. thanks claudia
2013/4/29 Claudia Dacquino <claudia.dacqu...@gmail.com> > 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. >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >
_______________________________________________ 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.
