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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