mris_fix_topology taking ages

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Ellen Ji

31 May 2021 31 May '21

11:16 a.m.

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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_F..., 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

Attachments:

mris_fix_topology.txt (text/plain — 20.8 KB)

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Douglas N. Greve

31 May 31 May

8:51 p.m.

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_F..., 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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Ellen Ji

1 Jun 1 Jun

4:55 p.m.

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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_F..., 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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Douglas N. Greve

5:56 p.m.

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_F..., 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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Fischl, Bruce

9:11 p.m.

Or the ?h.inflated.nofix can be helpful as well

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, June 1, 2021 5:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology taking ages

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,

tksurfer avoss_01 lh defect_labels

No such file or directory

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DIANA ORTEGA CRUZ

2 Jun 2 Jun

3:12 a.m.

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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 (BFISCHL@mgh.harvard.edu) escribió:

...

Or the ?h.inflated.nofix can be helpful as well

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve *Sent:* Tuesday, June 1, 2021 5:57 PM *To:* 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_F..., 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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Fischl, Bruce

10:40 a.m.

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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,

Thanks a lot for your great help!! Best wishes, Diana Ortega.

El mié, 2 jun 2021 a las 3:13, Fischl, Bruce (<BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu>) escribió: Or the ?h.inflated.nofix can be helpful as well

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve Sent: Tuesday, June 1, 2021 5:57 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology taking ages

tksurfer avoss_01 lh defect_labels

No such file or directory

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Ellen Ji

12:18 p.m.

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

Cheers

Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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,

Thanks a lot for your great help!! Best wishes,

Diana Ortega.

El mié, 2 jun 2021 a las 3:13, Fischl, Bruce (<BFISCHL@mgh.harvard.edu mailto:BFISCHL@mgh.harvard.edu>) escribió:

Or the ?h.inflated.nofix can be helpful as well

*From:* freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@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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participants (4)

DIANA ORTEGA CRUZ
Douglas N. Greve
Ellen Ji
Fischl, Bruce