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 <fis...@nmr.mgh.harvard.edu>
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
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