Can you send us specific coordinates of things to look at? > On Oct 24, 2016, at 10:44 PM, Cong <3110103...@zju.edu.cn> wrote: > > Hi Dear Bruce > I have uploaded a subject named Cong2Bruce.zip through ftp. I can’t fix > it by myself. Could you help me how to use expert options to get correct > white matter and gray matter surface. Thank you very much. > > Best Wished > Cong Chen > >> Date: Tue, 20 Sep 2016 10:45:30 -0400 (EDT) >> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] White matter surface don't change after >> editing >> >> Hi Cong >> >> we are experiencing serious disk problems at Martinos, so the ftp site is >> down. >> >> Try changing the values for mri_segment also. Note that what you are >> seeing are NOT topological defects as mris_make_surfaces preserves the >> input topology whatever its settings. Make sure to look in 3D and scoll >> through your slices. You can also try changing the gm thresholds >> >> cheers >> Bruce >> >>> On Tue, 20 Sep 2016, Cong wrote: >>> >>> Hi Dear Bruce >>> ? ? ?Thanks very much for your reply, I ?improved min_border_white to >>> 100, the lh.white line shrinks but still is far out in some area, ?and >>> I notice many topological defect appears as a result. >>> ? ? ?I failed to upload subject through ftp, it's always appear an >>> error called "550 Failed to change directory", so I send a subject to >>> you through FileDrop. Can you receive a file named Cong2Bruce.zip?? >>> >>> ? ? ?Thanks again for your help. >>> >>> Best Wishes >>> Cong Chen >>> >>> Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT) >>> From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>> Hi Cong >>> >>> you could try using expert options to modify the >>> mris_make_surfaces? >>> parameters. It looks like you white surface is too far out. Try? >>> increasing min_border_white and/or increasing max_gray. If you >>> can't get it? >>> working feel free to upload the entire subject dir and we will >>> take a look >>> >>> cheers >>> Bruce >>> >>> >>> On Thu, 8 Sep 2016, Cong wrote: >>> >>> Hi dear all >>> ? ? I attach a new picture to illustrate this problem. ?I erased >>> some voxels in wm.mgz and rerun. The lh.orig(blue line) looks >>> well, but lh.white(yellow line) don?t along the white surface in >>> some area. Could anyone give me some advice? Thanks very much. >>> >>> Best wishes >>> Cong Chen >>> >>> >>> Date: Sun, 4 Sep 2016 15:15:42 +0800 >>> From: Cong <3110103...@zju.edu.cn> >>> Subject: [Freesurfer] White matter surface don't change after >>> editing >>> >>> Dear freesurfer team? >>> ?I have some MRI images from a GE scanner, ?it seems that >>> images? quality is poor because grey matter is bright in so much >>> area and these grey matter is included in wm.mgz. So I deleted >>> wrong voxels in wm.mgz by freeview and rerun through command ? >>> recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But >>> ?h.white (yellow line) don?t change after rerunning as you can >>> see in the attached picture. ?Is this problem caused by deleting >>> too many voxels and how to fix it? ?Thanks very much. >>> >>> Regards >>> Cong Chen > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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