yes. The only time I've seen this error is when the surface file didn't finish writing. You can load the defects with something like:
tksurfer -orig orig.nofix $subject $hemi inflated.nofix
then load the curvature file $hemi.defect_labels. You should be able to use save point/goto point in tksurfer and tkmedit to figure out where each vertex is in the wm.mgz volume and manually correct it (although this is an acquired skill!). You may need to specifiy -white orig.nofix as well, although looking at the code I don't think you do.
cheers, Bruce
On Thu, 20 Aug 2009, Falk Lüsebrink wrote:
Hi Bruce,
No, there are some hundreds of GB left.
Is the other topology fixer you meant before mris_topo_fixer?
Thanks in advance, Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, August 20, 2009 4:44 AM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu; 'Douglas N Greve' Subject: Re: [Freesurfer] mris_fix_topology
are you out of disk space? On Thu, 20 Aug 2009, Falk Lüsebrink wrote:
Hi Doug,
I get the following error:
rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face list
Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, August 20, 2009 12:12 AM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology
It was not mris_fix_topology that failed but mris_euler_number (but that might have failed because of something in the topology fix). What happens if you:
cd /home/falk/freesurfer/subjects/yv98_05mm_div mris_euler_number ../surf/rh.orig
doug
Falk Lüsebrink wrote:
Hi FreeSurfers,
Attached is a log file containing an error of mris_fix_topology and I would like to know how to fix that issue if that is possible. Is it possible to view a defect (in that case #33) in tksurfer or freeview to identify a possible error in the wm.mgz or filled.mgz to correct it manually?
Thanks in advance,
Falk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, I'll try to do that.
Are the commands for mris_topo_fixer the same as of mris_fix_topology? I haven't seen a help for that one.
Regards, Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, August 20, 2009 2:36 PM To: Falk Lüsebrink Cc: freesurfer@surfer.nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology
yes. The only time I've seen this error is when the surface file didn't finish writing. You can load the defects with something like:
tksurfer -orig orig.nofix $subject $hemi inflated.nofix
then load the curvature file $hemi.defect_labels. You should be able to use save point/goto point in tksurfer and tkmedit to figure out where each vertex is in the wm.mgz volume and manually correct it (although this is an acquired skill!). You may need to specifiy -white orig.nofix as well, although looking at the code I don't think you do.
cheers, Bruce
On Thu, 20 Aug 2009, Falk Lüsebrink wrote:
Hi Bruce,
No, there are some hundreds of GB left.
Is the other topology fixer you meant before mris_topo_fixer?
Thanks in advance, Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, August 20, 2009 4:44 AM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu; 'Douglas N Greve' Subject: Re: [Freesurfer] mris_fix_topology
are you out of disk space? On Thu, 20 Aug 2009, Falk Lüsebrink wrote:
Hi Doug,
I get the following error:
rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face list
Falk
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, August 20, 2009 12:12 AM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology
It was not mris_fix_topology that failed but mris_euler_number (but that might have failed because of something in the topology fix). What happens if you:
cd /home/falk/freesurfer/subjects/yv98_05mm_div mris_euler_number ../surf/rh.orig
doug
Falk Lüsebrink wrote:
Hi FreeSurfers,
Attached is a log file containing an error of mris_fix_topology and I would like to know how to fix that issue if that is possible. Is it possible to view a defect (in that case #33) in tksurfer or freeview to identify a possible error in the wm.mgz or filled.mgz to correct it manually?
Thanks in advance,
Falk
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Falk Lüsebrink