On Sep 10, 2016, at 1:15 AM, 3110103623@zju.edu.cn 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 "553 Could not create file", 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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <3110103623@zju.edu.cn mailto:3110103623@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
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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <3110103623@zju.edu.cn mailto:3110103623@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
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 BruceThanks 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 fischl@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 3110103623@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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Cong