[Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Ione Fine]

Hi, 

I am running to an error analyzing a 0.5 mm resolution T1 structural with
the following with the following:

recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT

 

the issue seems to be:

mri_tessellate: max vertices 100 exceeded

 

There's apparently a version of mri_tesselate which is easier going about
the number of vertices, but the link to it is broken.

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/040001.htm
l

 

Thanks

Ione

 

System information:

 

FREESURFER_HOME: /usr/local/freesurfer/stable5_3

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Debian version: 7.6

Kernel info: Linux 3.2.0-4-amd64 x86_64

 

 

 

 

Professor of Psychology

University of Washington

http://faculty.washington.edu/ionefine/

 

 

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[Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Ione Fine]

 

 

Lovely experts,

 

I am running to an error analyzing a 0.5 mm resolution T1 structural with
the following with the following command:

recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT

 

the issue seems to be:

mri_tessellate: max vertices 100 exceeded

 

There's apparently a version of mri_tesselate which is more lax about the
number of vertices, but the link to it is broken.

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/040001.htm
l

 

Thanks

Ione

 

System information:

 

FREESURFER_HOME: /usr/local/freesurfer/stable5_3

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Debian version: 7.6

Kernel info: Linux 3.2.0-4-amd64 x86_64

 

 

 

 

Ione Fine

Professor of Psychology

University of Washington

http://faculty.washington.edu/ionefine/

 

 

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[Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Michiel Kleinnijenhuis]

Hi,

While doing a high resolution ex vivo recon job, I came across the error
mri_tessellate: max vertices 100 exceeded

As mentioned in the threads
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html
there seems to be an easy fix.

Does anyone have a compiled version of mri_tesselate with the vertex limit 
relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)?

Thanks!
Michiel Kleinnijenhuis

==
Michiel Kleinnijenhuis
Postdoctoral researcher
FMRIB Centre
Nuffield Department of Clinical Neurosciences
University of Oxford


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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Bruce Fischl]

Hi Iona

if you tell us what your hardware/software environment is we'll get you a 
newer version.


cheers
Bruce
On Sat, 11 Jul 2015, Ione Fine wrote:



Hi,

I am running to an error analyzing a 0.5 mm resolution T1 structural with the
following with the following:

recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT

 

the issue seems to be:

mri_tessellate: max vertices 100 exceeded

 

There’s apparently a version of mri_tesselate which is easier going about the
number of vertices, but the link to it is broken.

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/040001.html

 

Thanks

Ione

 

System information:

 

FREESURFER_HOME: /usr/local/freesurfer/stable5_3

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Debian version: 7.6

Kernel info: Linux 3.2.0-4-amd64 x86_64

 

 

 

 

Professor of Psychology

University of Washington

http://faculty.washington.edu/ionefine/

 

 


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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Ione Fine]

I think the info was at the end of the email, as per instructions. Is there
any other info you need?

Thanks!
Ione

FREESURFER_HOME: /usr/local/freesurfer/stable5_3

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Debian version: 7.6

Kernel info: Linux 3.2.0-4-amd64 x86_64


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Saturday, July 11, 2015 3:01 PM
To: ionef...@uw.edu; Freesurfer support list
Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded

Hi Iona

if you tell us what your hardware/software environment is we'll get you a
newer version.

cheers
Bruce
On Sat, 11 Jul 2015, Ione Fine wrote:

> 
> Hi,
> 
> I am running to an error analyzing a 0.5 mm resolution T1 structural 
> with the following with the following:
> 
> recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT
> 
>  
> 
> the issue seems to be:
> 
> mri_tessellate: max vertices 100 exceeded
> 
>  
> 
> There?s apparently a version of mri_tesselate which is easier going 
> about the number of vertices, but the link to it is broken.
> 
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400
> 01.html
> 
>  
> 
> Thanks
> 
> Ione
> 
>  
> 
> System information:
> 
>  
> 
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3
> 
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> 
> Debian version: 7.6
> 
> Kernel info: Linux 3.2.0-4-amd64 x86_64
> 
>  
> 
>  
> 
>  
> 
>  
> 
> Professor of Psychology
> 
> University of Washington
> 
> http://faculty.washington.edu/ionefine/
> 
>  
> 
>  
> 
> 
>


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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Ione Fine]

FREESURFER_HOME: /usr/local/freesurfer/stable5_3
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: 7.6
Kernel info: Linux 3.2.0-4-amd64 x86_64

I think the info was at the end of the original email, as per instructions. 

I'm guessing it was just hidden, but let me know if there's any other info
you need?

Thanks!
Ione


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Saturday, July 11, 2015 3:01 PM
To: ionef...@uw.edu; Freesurfer support list
Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded

Hi Iona

if you tell us what your hardware/software environment is we'll get you a
newer version.

cheers
Bruce
On Sat, 11 Jul 2015, Ione Fine wrote:

> 
> Hi,
> 
> I am running to an error analyzing a 0.5 mm resolution T1 structural 
> with the following with the following:
> 
> recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT
> 
>  
> 
> the issue seems to be:
> 
> mri_tessellate: max vertices 100 exceeded
> 
>  
> 
> There?s apparently a version of mri_tesselate which is easier going 
> about the number of vertices, but the link to it is broken.
> 
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400
> 01.html
> 
>  
> 
> Thanks
> 
> Ione
> 
>  
> 
> System information:
> 
>  
> 
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3
> 
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> 
> Debian version: 7.6
> 
> Kernel info: Linux 3.2.0-4-amd64 x86_64
> 
>  
> 
>  
> 
>  
> 
>  
> 
> Professor of Psychology
> 
> University of Washington
> 
> http://faculty.washington.edu/ionefine/
> 
>  
> 
>  
> 
> 
>


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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[zkaufman]

Hello,

Here is a download link to the most recent version of mri_tessellate:

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_tessellate

Please place the new version in your $FREESURFER_HOME/bin directory, and
backup the original. Hope this helps.

-Zeke

>
> FREESURFER_HOME: /usr/local/freesurfer/stable5_3
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Debian version: 7.6
> Kernel info: Linux 3.2.0-4-amd64 x86_64
>
> I think the info was at the end of the original email, as per
> instructions.
>
> I'm guessing it was just hidden, but let me know if there's any other info
> you need?
>
> Thanks!
> Ione
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Saturday, July 11, 2015 3:01 PM
> To: ionef...@uw.edu; Freesurfer support list
> Subject: Re: [Freesurfer] mri_tessellate: max vertices 100 exceeded
>
> Hi Iona
>
> if you tell us what your hardware/software environment is we'll get you a
> newer version.
>
> cheers
> Bruce
> On Sat, 11 Jul 2015, Ione Fine wrote:
>
>>
>> Hi,
>>
>> I am running to an error analyzing a 0.5 mm resolution T1 structural
>> with the following with the following:
>>
>> recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT
>>
>>  
>>
>> the issue seems to be:
>>
>> mri_tessellate: max vertices 100 exceeded
>>
>>  
>>
>> There?s apparently a version of mri_tesselate which is easier going
>> about the number of vertices, but the link to it is broken.
>>
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-August/0400
>> 01.html
>>
>>  
>>
>> Thanks
>>
>> Ione
>>
>>  
>>
>> System information:
>>
>>  
>>
>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3
>>
>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>>
>> Debian version: 7.6
>>
>> Kernel info: Linux 3.2.0-4-amd64 x86_64
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>> Professor of Psychology
>>
>> University of Washington
>>
>> http://faculty.washington.edu/ionefine/
>>
>>  
>>
>>  
>>
>>
>>
>
>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Partners
> Compliance
> HelpLine at http://www.partners.org/complianceline . If the e-mail was
> sent
> to you in error but does not contain patient information, please contact
> the
> sender and properly dispose of the e-mail.
>
>
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>
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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Ione Fine]

Hi,

I'm getting a new error
 
mri_tessellate: error while loading shared libraries: libnetcdf.so.6: cannot
open shared object file: No such file or directory
Linux dws-9 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u1 x86_64 GNU/Linux

For this particular library for Debian, there is *.so.5 and *.so.7.

Which should we use?

So many thanks for your help on this.

Ione


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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Z K]

I will have to investigate why this error is occurring as it shouldn't 
be happening. But regardless a quick fix should be to symlink to the 
*.so.7 as that is more likely to be backwards compatible:

$> cd /usr/lib64
$> sudo ln -s libnetcdf.so.7 libnetcdf.so.6

-Zeke

On 07/14/2015 12:59 PM, Ione Fine wrote:
> Hi,
>
> I'm getting a new error
>
> mri_tessellate: error while loading shared libraries: libnetcdf.so.6: cannot
> open shared object file: No such file or directory
> Linux dws-9 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u1 x86_64 GNU/Linux
>
> For this particular library for Debian, there is *.so.5 and *.so.7.
>
> Which should we use?
>
> So many thanks for your help on this.
>
> Ione
>
>
> ___
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>
>
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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Z K]

Hello,

The latest version of mri_tessellate can be downloaded using this the 
following link:

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate

It would be wise to backup your existing version befor overwriting it 
with the version contained in the link above.

-Zeke

On 08/19/2014 05:52 PM, Michiel Kleinnijenhuis wrote:
> Hi,
>
> While doing a high resolution ex vivo recon job, I came across the error
> mri_tessellate: max vertices 100 exceeded
>
> As mentioned in the threads
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html
> 
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html
> 
> there seems to be an easy fix.
>
> Does anyone have a compiled version of mri_tesselate with the vertex
> limit relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)?
>
> Thanks!
> Michiel Kleinnijenhuis
>
> ==
> *Michiel Kleinnijenhuis*
> Postdoctoral researcher
> FMRIB Centre
> Nuffield Department of Clinical Neurosciences
> University of Oxford
>
>
>
>
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>
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Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

[Bruce Fischl]

Thanks Zeke
Bruce

> On Aug 20, 2014, at 1:55 PM, Z K  wrote:
> 
> Hello,
> 
> The latest version of mri_tessellate can be downloaded using this the 
> following link:
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate
> 
> It would be wise to backup your existing version befor overwriting it 
> with the version contained in the link above.
> 
> -Zeke
> 
>> On 08/19/2014 05:52 PM, Michiel Kleinnijenhuis wrote:
>> Hi,
>> 
>> While doing a high resolution ex vivo recon job, I came across the error
>> mri_tessellate: max vertices 100 exceeded
>> 
>> As mentioned in the threads
>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html
>> 
>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html
>> 
>> there seems to be an easy fix.
>> 
>> Does anyone have a compiled version of mri_tesselate with the vertex
>> limit relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)?
>> 
>> Thanks!
>> Michiel Kleinnijenhuis
>> 
>> ==
>> *Michiel Kleinnijenhuis*
>> Postdoctoral researcher
>> FMRIB Centre
>> Nuffield Department of Clinical Neurosciences
>> University of Oxford
>> 
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
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> ___
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> 
> 

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