External Email - Use Caution
thanks Bruce and Douglas,
I was able to see the holes by looking at the surface of
?h.smoothwm.nofix and I found the Freesurfer tutorial on how to correct
topological defects.
However, as the automatic topology fixer runs during recon-all, how do
we know that it failed? I see "CORRECTING DEFECT" for multiple defects
in the recon-all.log, so I'm assuming it's fixing those holes.
How can I determine whether it's worth it to go in and manually fix
them? Is there an indication somewhere?
Thank you!
On 6/2/2021 4:40 PM, Fischl, Bruce wrote:
Hi Diana
It’s not the number of defects that matters – it is the large ones.
The time it takes to correct them is square in the (convex hull of
the) number of vertices in the defect. We have a tutorial on our
website about how to find them and fix them. I find it easiest to load
the ?h.orig.nofix over the wm.mgz and norm.mgz then load the
?h.defect_labels to onto the ?h.orig.nofix to color the vertices that
are in a defect
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *DIANA ORTEGA CRUZ
*Sent:* Wednesday, June 2, 2021 3:12 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mris_fix_topology taking ages
* External Email - Use Caution *
Dear Douglas and Bruce,
my name is Diana, I am encountering the same issue as Ellen with
Fix-topology taking too long. Once we make sense of the origin of the
issue (for example, I confirmed that my smoothwm.nofix has a lot of
holes), do you know if is there any way to solve it? Could the data be
modified in some way to get through this step?
Thanks a lot for your great help!! Best wishes,
Diana Ortega.
El mié, 2 jun 2021 a las 3:13, Fischl, Bruce (<bfis...@mgh.harvard.edu
<mailto:bfis...@mgh.harvard.edu>>) escribió:
Or the ?h.inflated.nofix can be helpful as well
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Douglas N. Greve
*Sent:* Tuesday, June 1, 2021 5:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mris_fix_topology taking ages
I mean mris_fix_topology. Try loading the ?h.smoothwm.nofix in
surface viewing (not in the volume). You can often see defects
better on this surface (they look likes holes or handles; you
should at least see some)
On 6/1/2021 4:55 PM, Ellen Ji wrote:
* External Email - Use Caution *
Hi Doug, when you say it did not finish, could you clarify
what process "it" refers to?
I loaded the files you suggested and nothing popped out to me
aside from the fact that the wm.mgz didn't seem to cover all
the white matter.
Is it possible that topology error labels don't necessarily
suggest that something went wrong and I can trust the results?
Thanks.
On 6/1/2021 2:51 AM, Douglas N. Greve wrote:
The topology error labels might be be created if it did
not finish. YOu can try just loading the brain.mgz, the
wm.mgz, and the orig.nofix and see if you can find a big
topo error
On 5/31/2021 11:16 AM, Ellen Ji wrote:
External Email - Use Caution
Dear experts,
mris_fix_topology has been running for several hours
now and the log suggests many more defects than
normal. I tried to follow Bruce's advice from the
thread here
https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html
<https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html>,
but wasn't able to load the &h.defect_labels as I
received the error below.
Attached is part of the recon-all.log (starting from
mris_fix_topology). Is there any other way to
check/visualize what might have gone wrong?
FYI, I'm running recon-all thru the HCP Pipeline. Thanks!
tksurfer avoss_01 lh defect_labels
subject is avoss_01
hemi is lh
surface is defect_labels
surfer: current subjects dir:
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w
surfer: not in "scripts" dir ==> using cwd for session
root
surfer: session root data dir ($session) set to:
surfer:
/mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf
checking for nofix files in 'defect_labels'
Reading image info
(/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01)
Reading
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
surfer: Reading header info from
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
nquads=4063237, nvertices=664
ERROR: MRISread: file
'/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels'
has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
No such file or directory
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