Hi Dear Bruce My problem is bilateral high signal grey matter in T1 image. For example, in uploaded subject at coordinate of TkReg RAS -59.00 3.00 5.00, white matter surface is too far out even though I have erased extra white matter voxel in wm.mgz and rerun. Another problem is grey matter surface bend inward, for example at coordinate of TkReg RAS -61.00 3.00 -14.00. I tried to use expert options to improve min_border_white and max_gray but couldn’t get satisfied surface. So I want to know whether freesurfer can fix these two problems and how. I’m sorry to occupy you so much time. Thanks very much.
Best Wishes Cong Chen
Date: Mon, 24 Oct 2016 23:22:58 -0400 From: Bruce Fischl fischl@nmr.mgh.harvard.edu
Can you send us specific coordinates of things to look at?
On Oct 24, 2016, at 10:44 PM, Cong 3110103623@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 fischl@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 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
Hi Cong
looking at your original data there is simply no contrast in the gray matter in those regions. I'm not sure why this would be the case, but it isn't recoverable as the images don't contain any information that we can use - the gray matter there is uniformly brighter than the white matter. It looks like some kind of coil issue as it is spatially localized, although it is true in the right hemi as well. If you give us the details of your acquisition we might be able to help in the future, but with these images you won't be able to get any reliable thickness/volume info in those spots. That said, the recon did a surprisingly good job at building accurate surfaces despite these artifacts, so they should still provide usable information elsewhere
cheers Bruce
On Wed, 26 Oct 2016, Cong wrote:
Hi Dear Bruce My problem is bilateral high signal grey matter in T1 image. For example, in uploaded subject at coordinate of TkReg RAS -59.00 3.00 5.00, white matter surface is too far out even though I have erased extra white matter voxel in wm.mgz and rerun. Another problem is grey matter surface bend inward, for example at coordinate of TkReg RAS -61.00 3.00 -14.00. I tried to use expert options to improve min_border_white and max_gray but couldn’t get satisfied surface. So I want to know whether freesurfer can fix these two problems and how. I’m sorry to occupy you so much time. Thanks very much.
Best Wishes Cong Chen
Date: Mon, 24 Oct 2016 23:22:58 -0400 From: Bruce Fischl fischl@nmr.mgh.harvard.edu
Can you send us specific coordinates of things to look at?
On Oct 24, 2016, at 10:44 PM, Cong 3110103623@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 fischl@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 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
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