[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] Load a .label as a mask in tksurfer

[LiuKai]

Dear experts,Is there a way in tksurfer which could enable us to load a surface 
mask (e.g., lh.cortex.label) to confine the visualization of annotation files 
within certain cortical region? For example, now I want to confine the 
visualization of brain surface values within cortex (with corpus callosum etc. 
exluded), and I have tried to load the lh.cortex.label as a filed mask, while 
it seemed not work. Besides, I also tried the -mask option in command line, it 
seemed that this option didn't accept a .label file.So, how should a add a 
certain .label file as a mask in tksurfer?Thank you!!kaiThe Chinese University 
of Hong Kong   ___
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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] voxel of different size

[Sandro Marini]

Dear FreeSurfer experts,
we have collected some data with different voxel size (from 0.78 to 0.94 mm
iso). I would like to do an analysis of all these scans. Is it possible ?
Should I use -cw256 option to make the sample uniform?

Many thanks
Best,

Sandro
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Re: [Freesurfer] Regarding: Brainstem substructures

[Bruce Fischl]

Hi Sampada

the brainstem stuff was developed after 5.3 so it is likely not in the 
version you have. Eugenio or Zeke can point you in the right direction.

cheers
Bruce


On Sat, 11 Jul 2015, Dr Sampada Sinha 
wrote:

> Dear freesurfer experts,
> 
> I am trying to do the brainstem volumetric analysis especially of the 
> medullary
> region. My recon-all command ran successfully and now when I am trying to run 
> the
> command ' recon-all -s IMRAN -brainstem-structures'
> (https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures) but, I get 
> the
> following error:
> 
> 
> ERROR: Flag -brainstem-structures unrecognized.
> -s IMRAN -brainstem-structures
> Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 
> UTC
> 2013 x86_64 x86_64 x86_64 GNU/Linux
> 
> Will you please let me know where I am going wrong? I am using the
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> version for my analysis.
> 
> Thanks for your time!
> 
> Kind regards,
> 
> Sampada
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>
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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] Load a .label as a mask in tksurfer

[Bruce Fischl]

Hi Kai

try the mask_label command from the tcl prompt.

cheers
Bruce



On Sat, 11 Jul 2015, LiuKai wrote:


Dear experts,
Is there a way in tksurfer which could enable us to load a surface mask (e.g.,
lh.cortex.label) to confine the visualization of annotation files within certain
cortical region? 

For example, now I want to confine the visualization of brain surface values
within cortex (with corpus callosum etc. exluded), and I have tried to load
the lh.cortex.label as a filed mask, while it seemed not work. Besides, I also
tried the -mask option in command line, it seemed that this option didn't 
accept a
.label file.

So, how should a add a certain .label file as a mask in tksurfer?

Thank you!!

kai

The Chinese University of Hong Kong

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Re: [Freesurfer] voxel of different size

[Bruce Fischl]

Hi Sandro

can you clarify what you mean? Do you want to run recon-all on each one 
separately? That would be fine. Or do you mean somehow average all the 
different res volumes into a single recon?


cheers
Bruce


On Sat, 11 Jul 2015, Sandro 
Marini wrote:



Dear FreeSurfer experts,
we have collected some data with different voxel size (from 0.78 to 0.94 mm 
iso).
I would like to do an analysis of all these scans. Is it possible ? Should I use
-cw256 option to make the sample uniform?

Many thanks
Best,

Sandro

 

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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] Regarding: Brainstem substructures

[Dr Sampada Sinha]

​Thanks so much Bruce for ​your reply. when I open the link for brain stem
structures (https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures),
it says "*This functionality is present in FreeSurfer
 6.0 and later*" .
And, when I go to the freesurfer download page, the only latest version of
freesurfer (last updated by Zeke on 2015-06-02) I see is stable v5.3.0. If
the version 6.0 is out, will you please send me the link so that I can
download it?

Thanks and regards,

Sampada

On Sat, Jul 11, 2015 at 7:30 PM, Bruce Fischl 
wrote:

> Hi Sampada
>
> the brainstem stuff was developed after 5.3 so it is likely not in the
> version you have. Eugenio or Zeke can point you in the right direction.
>
> cheers
> Bruce
>
>
> On Sat, 11 Jul 2015, Dr Sampada Sinha
> wrote:
>
> > Dear freesurfer experts,
> >
> > I am trying to do the brainstem volumetric analysis especially of the
> medullary
> > region. My recon-all command ran successfully and now when I am trying
> to run the
> > command ' recon-all -s IMRAN -brainstem-structures'
> > (https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures) but,
> I get the
> > following error:
> >
> >
> > ERROR: Flag -brainstem-structures unrecognized.
> > -s IMRAN -brainstem-structures
> > Linux localhost.localdomain 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22
> 03:15:09 UTC
> > 2013 x86_64 x86_64 x86_64 GNU/Linux
> >
> > Will you please let me know where I am going wrong? I am using the
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > version for my analysis.
> >
> > Thanks for your time!
> >
> > Kind regards,
> >
> > Sampada
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> ___
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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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Freesurfer Digest, Vol 137, Issue 13

[Sandro Marini]

Hi Bruce,
Thanks for your help. Yes, I would like to run recon-all on each one
separately and then use all the output data irrespective of the original
MRI voxel size. In other words, do the output values (i.e white matter
volume) depend on the voxel size of the original MRI?
Best,

Sandro

Message: 11

> Date: Sat, 11 Jul 2015 10:04:20 -0400 (EDT)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] voxel of different size
> To: Freesurfer support list 
> Message-ID:
> 
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sandro
>
> can you clarify what you mean? Do you want to run recon-all on each one
> separately? That would be fine. Or do you mean somehow average all the
> different res volumes into a single recon?
>
> cheers
> Bruce
>
>
> On Sat, 11 Jul 2015, Sandro
> Marini wrote:
>
> > Dear FreeSurfer experts,
> > we have collected some data with different voxel size (from 0.78 to 0.94
> mm iso).
> > I would like to do an analysis of all these scans. Is it possible ?
> Should I use
> > -cw256 option to make the sample uniform?
> >
> > Many thanks
> > Best,
> >
> > Sandro
>
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Re: [Freesurfer] Freesurfer Digest, Vol 137, Issue 13

[Bruce Fischl]

Hi Sandro

yes, you will find some dependence. Much as we would like it to be 
otherwise when you change resolution you change a bunch of other things 
typically (min TE, bandwidth, big SNR changes) that will cause changes in 
our measured volumes


cheers
Bruce


On Sat, 11 Jul 2015, Sandro Marini wrote:


Hi Bruce,
Thanks for your help. Yes, I would like to run recon-all on each one
separately and then use all the output data irrespective of the original MRI
voxel size. In other words, do the output values (i.e white matter volume)
depend on the voxel size of the original MRI?
Best,

Sandro

Message: 11
  Date: Sat, 11 Jul 2015 10:04:20 -0400 (EDT)
  From: Bruce Fischl 
  Subject: Re: [Freesurfer] voxel of different size
  To: Freesurfer support list 
  Message-ID:
         
  
  Content-Type: text/plain; charset="utf-8"

  Hi Sandro

  can you clarify what you mean? Do you want to run recon-all on
  each one
  separately? That would be fine. Or do you mean somehow average
  all the
  different res volumes into a single recon?

  cheers
  Bruce


  On Sat, 11 Jul 2015, Sandro
  Marini wrote:

  > Dear FreeSurfer experts,
  > we have collected some data with different voxel size (from
  0.78 to 0.94 mm iso).
  > I would like to do an analysis of all these scans. Is it
  possible ? Should I use
  > -cw256 option to make the sample uniform?
  >
  > Many thanks
  > Best,
  >
  > Sandro


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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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