Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

Hi Gabriel

they are in the subject's directory. Have you gone through the FS 
tutorials on our wiki? That would be a good place to start


cheers
Bruce
On Tue, 25 Feb 2020, Gabriel Tapia wrote:



External Email - Use Caution

Hello Bruce thank you for your quick reply,
Where should I look to get all these files?
The idea to check them is to confirm that the MRI went wrong at some point,
right?
Thanks,

Gabriel Tapia
www.Partage3D.fr
+33 6 62 90 11 67


Le mar. 25 févr. 2020 à 04:09, Bruce Fischl  a
écrit :
  Hi Gabriel,

  that is a huge defect and generally means something major has
  gone wrong.
  Look at the lh or rh.orig.nofix and the corresponding
  ?h.inflated.nofix
  over the wm.mgz file to see what is wrong (usually something
  like a big
  chunk of skull is left over and connected to the surface,
  sometimes
  through orbital fat in the eye sockets)

  If you can't sort it out let us know and we will help
  cheers
  Bruce

  On Tue, 25 Feb 2020, Gabriel Tapia
  wrote:

  >
  > External Email - Use Caution
  >
  > Hello dear Freesurfer developers, nice to e-meet you and thank
  you for
  > working on this open source software!
  >
  > I am trying to produce a 3D file of a brain.
  > The command I am trying to run is recon-all and here is the
  error I get:
  > CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
  > Excessive topologic defect encountered: could not allocate
  140742253
  > edges for retessellation
  > Cannot allocate memory
  >
  > The version I am using is:
  freesurfer-Linux-centos4-stable-pub-v5.3.0
  > The platform is Red Hat 64-bit running in a Virtual box with
  7835mb
  > allocated memory.
  > You will find the corresponding log file attached.
  >
  > Isn't it surprising that I don't have enough memory with
  7835mb allocated?
  > Sorry, I am new to Freesurfer and there might be something I
  didn't get.
  > Thank you very much in advance for your help,
  > Regards,
  >
  > Gabriel Tapia
  > www.Partage3D.fr
  > +33 6 62 90 11 67
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Cannot allocate memory

[Tim Schäfer]

External Email - Use Caution

They are all in the output folder of the subject.

The noxfix files are surfaces (in /surf/), the mgz file is a volume 
(in /mri/).

Tim

> On February 25, 2020 at 4:24 AM Gabriel Tapia  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello Bruce thank you for your quick reply,
> Where should I look to get all these files?
> The idea to check them is to confirm that the MRI went wrong at some point,
> right?
> Thanks,
> 
> Gabriel Tapia 
> www.Partage3D.fr 
> +33 6 62 90 11 67
> 
> 
> Le mar. 25 févr. 2020 à 04:09, Bruce Fischl  a
> écrit :
> 
> > Hi Gabriel,
> >
> > that is a huge defect and generally means something major has gone wrong.
> > Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix
> > over the wm.mgz file to see what is wrong (usually something like a big
> > chunk of skull is left over and connected to the surface, sometimes
> > through orbital fat in the eye sockets)
> >
> > If you can't sort it out let us know and we will help
> > cheers
> > Bruce
> >
> > On Tue, 25 Feb 2020, Gabriel Tapia
> > wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > Hello dear Freesurfer developers, nice to e-meet you and thank you for
> > > working on this open source software!
> > >
> > > I am trying to produce a 3D file of a brain.
> > > The command I am trying to run is recon-all and here is the error I get:
> > > CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
> > > Excessive topologic defect encountered: could not allocate 140742253
> > > edges for retessellation
> > > Cannot allocate memory
> > >
> > > The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
> > > The platform is Red Hat 64-bit running in a Virtual box with 7835mb
> > > allocated memory.
> > > You will find the corresponding log file attached.
> > >
> > > Isn't it surprising that I don't have enough memory with 7835mb
> > allocated?
> > > Sorry, I am new to Freesurfer and there might be something I didn't get.
> > > Thank you very much in advance for your help,
> > > Regards,
> > >
> > > Gabriel Tapia
> > > www.Partage3D.fr
> > > +33 6 62 90 11 67
> > >
> > >___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Cannot allocate memory

[Gabriel Tapia]

External Email - Use Caution

Hello Bruce thank you for your quick reply,
Where should I look to get all these files?
The idea to check them is to confirm that the MRI went wrong at some point,
right?
Thanks,

Gabriel Tapia 
www.Partage3D.fr 
+33 6 62 90 11 67


Le mar. 25 févr. 2020 à 04:09, Bruce Fischl  a
écrit :

> Hi Gabriel,
>
> that is a huge defect and generally means something major has gone wrong.
> Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix
> over the wm.mgz file to see what is wrong (usually something like a big
> chunk of skull is left over and connected to the surface, sometimes
> through orbital fat in the eye sockets)
>
> If you can't sort it out let us know and we will help
> cheers
> Bruce
>
> On Tue, 25 Feb 2020, Gabriel Tapia
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello dear Freesurfer developers, nice to e-meet you and thank you for
> > working on this open source software!
> >
> > I am trying to produce a 3D file of a brain.
> > The command I am trying to run is recon-all and here is the error I get:
> > CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
> > Excessive topologic defect encountered: could not allocate 140742253
> > edges for retessellation
> > Cannot allocate memory
> >
> > The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
> > The platform is Red Hat 64-bit running in a Virtual box with 7835mb
> > allocated memory.
> > You will find the corresponding log file attached.
> >
> > Isn't it surprising that I don't have enough memory with 7835mb
> allocated?
> > Sorry, I am new to Freesurfer and there might be something I didn't get.
> > Thank you very much in advance for your help,
> > Regards,
> >
> > Gabriel Tapia
> > www.Partage3D.fr
> > +33 6 62 90 11 67
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

Hi Gabriel,

that is a huge defect and generally means something major has gone wrong. 
Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix 
over the wm.mgz file to see what is wrong (usually something like a big 
chunk of skull is left over and connected to the surface, sometimes 
through orbital fat in the eye sockets)


If you can't sort it out let us know and we will help
cheers
Bruce

On Tue, 25 Feb 2020, Gabriel Tapia 
wrote:




External Email - Use Caution

Hello dear Freesurfer developers, nice to e-meet you and thank you for
working on this open source software!

I am trying to produce a 3D file of a brain.
The command I am trying to run is recon-all and here is the error I get:
CORRECTING DEFECT 57 (vertices=33394, convex hull=9966)
Excessive topologic defect encountered: could not allocate 140742253
edges for retessellation
Cannot allocate memory

The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
The platform is Red Hat 64-bit running in a Virtual box with 7835mb
allocated memory.
You will find the corresponding log file attached.

Isn't it surprising that I don't have enough memory with 7835mb allocated?
Sorry, I am new to Freesurfer and there might be something I didn't get.
Thank you very much in advance for your help,
Regards,

Gabriel Tapia
www.Partage3D.fr
+33 6 62 90 11 67

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Cannot allocate memory

[Gabriel Tapia]

External Email - Use Caution

Hello dear Freesurfer developers, nice to e-meet you and thank you for
working on this open source software!

I am trying to produce a 3D file of a brain.
The command I am trying to run is recon-all and here is the error I get:



*CORRECTING DEFECT 57 (vertices=33394, convex hull=9966) Excessive
topologic defect encountered: could not allocate 140742253 edges for
retessellation Cannot allocate memory*

The version I am using is: freesurfer-Linux-centos4-stable-pub-v5.3.0
The platform is Red Hat 64-bit running in a Virtual box with 7835mb
allocated memory.
You will find the corresponding log file attached.

Isn't it surprising that I don't have enough memory with 7835mb allocated?
Sorry, I am new to Freesurfer and there might be something I didn't get.
Thank you very much in advance for your help,
Regards,

Gabriel Tapia 
www.Partage3D.fr 
+33 6 62 90 11 67
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Cannot allocate memory error

[Bruce Fischl]

Hi Aziz

freeview is the tool for visualizing the data, so use it to examine the 
outputs of recon-all and figure out what is causing the big defect


cheers
Bruce
On Thu, 
12 Jan 2017, Aziz Nanthaamornphong wrote:



Hi Bruce,
So, I  should run the freeview after got those error messages. I will try. 

Thank you,
Aziz.

On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl 
wrote:
  Hi Aziz

  it will be in the subject's surf dir. You can visualize it via:

  freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix


  cheers
  Bruce


  On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:

Hi Bruce,
How can I look at inflated.nofix as you mentioned? I
think I ran recon-all
for the 001.mgz without other files. 

Best Regards,
Aziz.

On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl

wrote:
      Hi Aziz

      yes, you ran out of RAM. That said, a defect
with 66K vertices
      is pretty big - more than 1/3 of a typical
surface. You should
      check to make sure nothing big is wrong (hemis
attached, skull
      left around, etc). Look at the
inflated.nofix surface and it
      should be obvious what the defect is

      cheers
      Bruce
      On Thu, 12 Jan 2017, Aziz Nanthaamornphong
wrote:

            Hi experts,

            I ran the command

            $recon-all -all  -subjid 0696 

            I have got these error messages

            CORRECTING DEFECT 46 (vertices=66623,
convex
            hull=8931)
            Excessive topologic defect encountered:
could not
            allocate 322592700 edges
            for retessellation
            Cannot allocate memory

            Linux xubuntu-VirtualBox
3.2.0-23-generic #36-Ubuntu
            SMP Tue Apr 10 20:41:14
            UTC 2012 i686 i686 i386 GNU/Linux

            I am not sure if this problem came from
the
             insufficient memory on my
            computer. Otherwise, please let me
suggestions for
            solving this problem.

            Thank you,
            Aziz.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.




--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information
Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.




--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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, 

Re: [Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi Bruce,

So, I  should run the freeview after got those error messages. I will try.

Thank you,
Aziz.

On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl 
wrote:

> Hi Aziz
>
> it will be in the subject's surf dir. You can visualize it via:
>
> freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix
>
>
>
> cheers
> Bruce
>
>
> On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>
> Hi Bruce,
>> How can I look at inflated.nofix as you mentioned? I think I ran recon-all
>> for the 001.mgz without other files.
>>
>> Best Regards,
>> Aziz.
>>
>> On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl > >
>> wrote:
>>   Hi Aziz
>>
>>   yes, you ran out of RAM. That said, a defect with 66K vertices
>>   is pretty big - more than 1/3 of a typical surface. You should
>>   check to make sure nothing big is wrong (hemis attached, skull
>>   left around, etc). Look at the inflated.nofix surface and it
>>   should be obvious what the defect is
>>
>>   cheers
>>   Bruce
>>   On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>>
>> Hi experts,
>>
>> I ran the command
>>
>> $recon-all -all  -subjid 0696
>>
>> I have got these error messages
>>
>> CORRECTING DEFECT 46 (vertices=66623, convex
>> hull=8931)
>> Excessive topologic defect encountered: could not
>> allocate 322592700 edges
>> for retessellation
>> Cannot allocate memory
>>
>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu
>> SMP Tue Apr 10 20:41:14
>> UTC 2012 i686 i686 i386 GNU/Linux
>>
>> I am not sure if this problem came from the
>>  insufficient memory on my
>> computer. Otherwise, please let me suggestions for
>> solving this problem.
>>
>> Thank you,
>> Aziz.
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>>
>> Aziz Nanthaamornphong, Ph.D.,
>> Chair of Master of Science Program in Information Technology
>> Department of ICT
>> Faculty of Technology and Environment
>> Prince of Songkla University, Phuket Campus
>> +66 7627 6716 (v)
>> http://research.te.psu.ac.th/aziz
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory error

[Bruce Fischl]

Hi Aziz

it will be in the subject's surf dir. You can visualize it via:

freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix


cheers
Bruce


On Thu, 12 
Jan 2017, Aziz Nanthaamornphong wrote:



Hi Bruce,
How can I look at inflated.nofix as you mentioned? I think I ran recon-all
for the 001.mgz without other files. 

Best Regards,
Aziz.

On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl 
wrote:
  Hi Aziz

  yes, you ran out of RAM. That said, a defect with 66K vertices
  is pretty big - more than 1/3 of a typical surface. You should
  check to make sure nothing big is wrong (hemis attached, skull
  left around, etc). Look at the inflated.nofix surface and it
  should be obvious what the defect is

  cheers
  Bruce
  On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:

Hi experts,

I ran the command

$recon-all -all  -subjid 0696 

I have got these error messages

CORRECTING DEFECT 46 (vertices=66623, convex
hull=8931)
Excessive topologic defect encountered: could not
allocate 322592700 edges
for retessellation
Cannot allocate memory

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu
SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux

I am not sure if this problem came from the
 insufficient memory on my
computer. Otherwise, please let me suggestions for
solving this problem.

Thank you,
Aziz.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.




--

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi Bruce,

How can I look at inflated.nofix as you mentioned? I think I ran recon-all
for the 001.mgz without other files.

Best Regards,
Aziz.

On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl 
wrote:

> Hi Aziz
>
> yes, you ran out of RAM. That said, a defect with 66K vertices is pretty
> big - more than 1/3 of a typical surface. You should check to make sure
> nothing big is wrong (hemis attached, skull left around, etc). Look at
> the inflated.nofix surface and it should be obvious what the defect is
>
> cheers
> Bruce
>
> On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:
>
> Hi experts,
>>
>> I ran the command
>>
>> $recon-all -all  -subjid 0696
>>
>> I have got these error messages
>>
>> CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)
>> Excessive topologic defect encountered: could not allocate 322592700 edges
>> for retessellation
>> Cannot allocate memory
>>
>> Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
>> 20:41:14
>> UTC 2012 i686 i686 i386 GNU/Linux
>>
>> I am not sure if this problem came from the  insufficient memory on my
>> computer. Otherwise, please let me suggestions for solving this problem.
>>
>> Thank you,
>> Aziz.
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>


-- 

Aziz Nanthaamornphong, Ph.D.,
Chair of Master of Science Program in Information Technology
Department of ICT
Faculty of Technology and Environment
Prince of Songkla University, Phuket Campus
+66 7627 6716 (v)
http://research.te.psu.ac.th/aziz
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory error

[Bruce Fischl]

Hi Aziz

yes, you ran out of RAM. That said, a defect with 66K vertices is pretty 
big - more than 1/3 of a typical surface. You should check to make sure 
nothing big is wrong (hemis attached, skull left around, etc). Look 
at the inflated.nofix surface and it should be obvious what the defect is


cheers
Bruce
On 
Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote:



Hi experts,

I ran the command

$recon-all -all  -subjid 0696 

I have got these error messages

CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)
Excessive topologic defect encountered: could not allocate 322592700 edges
for retessellation
Cannot allocate memory

Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux

I am not sure if this problem came from the  insufficient memory on my
computer. Otherwise, please let me suggestions for solving this problem.

Thank you,
Aziz.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

[Freesurfer] Cannot allocate memory error

[Aziz Nanthaamornphong]

Hi experts,

I ran the command

$recon-all -all  -subjid 0696

I have got these error messages

*CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)*
*Excessive topologic defect encountered: could not allocate 322592700 edges
for retessellation*
*Cannot allocate memory*

*Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10
20:41:14 UTC 2012 i686 i686 i386 GNU/Linux*

I am not sure if this problem came from the  insufficient memory on my
computer. Otherwise, please let me suggestions for solving this problem.

Thank you,
Aziz.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

[Heidi Foo]

Thanks Douglas, it works now!

On Thu, Aug 25, 2016 at 6:45 AM, Douglas N Greve 
wrote:

> It actually looks like it might be a problem with your covariates.mat
> file (MatrixReadTxT error). Can you send that file?
>
>
> On 08/22/2016 10:06 PM, Heidi Foo wrote:
> > Dear FreeSurfer team,
> >
> > I am currently running mri_glmfir --eres-save using FreeSurfer 6.0.
> > However, there is an error saying "not enough memory to buffer." I
> > have attached the error log for your reference. Do you have any idea
> > how I can solve this problem?
> >
> > Thank you.
> >
> > Regards,
> > Heidi
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

[Douglas N Greve]

It actually looks like it might be a problem with your covariates.mat 
file (MatrixReadTxT error). Can you send that file?


On 08/22/2016 10:06 PM, Heidi Foo wrote:
> Dear FreeSurfer team,
>
> I am currently running mri_glmfir --eres-save using FreeSurfer 6.0. 
> However, there is an error saying "not enough memory to buffer." I 
> have attached the error log for your reference. Do you have any idea 
> how I can solve this problem?
>
> Thank you.
>
> Regards,
> Heidi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Hi Doug,

Thanks. I was wondering if you think this would do the job: 1) use
fmcpr.nii.gz   2) split it to 3d volumes  3) do mri_vol2vol for all the
volumes separely  4) concatenate the resampled volumes together to get a 4d
volume. If you don't think this is a good approach, I appreciate it if you
could walk me through the steps.

Thanks in advance for your help
Best regards,
Ehsan



On Tue, Mar 22, 2016 at 3:53 PM, Douglas N Greve 
wrote:

> The problem is not the command, it is the size of the data it generates.
> You can try reducing the size of the anatomical to a bounding box around
> the brain. This is a bit tricky as you also have to compute a new
> registration. I can help step you through the process if you want to go
> in that direction.
>
> On 03/22/2016 11:50 AM, Ehsan Tadayon wrote:
> > Hi Doug,
> >
> > Thanks for your response. What I'm trying to do is to get each voxel's
> > times course in structural space and I was under the impression that
> > mri_vol2vol --mov func.nii would be the right way to go. Would you
> > please let me know what the best way would be to do this?
> >
> > best,
> > Ehsan,.
> >
> >
> > On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve
> > > wrote:
> >
> > that's going to create a pretty big volume as it will map your
> > functional time course to a 256^3 float volume. If you have 100
> > time points, then that will be about 7G.
> >
> > On 3/16/16 3:27 PM, Ehsan Tadayon wrote:
> >> Hi Bruce,
> >>
> >> Thanks for your response. I'm using :
> >>
> >> freesurfer version:
> >> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite
> >> 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using:
> >>
> >> mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
> >> func.anat.nii.gz
> >>
> >> Thanks in advance for your help.
> >>
> >> best regards,
> >> Ehsan.
> >>
> >>
> >>
> >>
> >> On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl
> >> >
> >> wrote:
> >>
> >> Hi Ehsan
> >>
> >> We need the full command line and screen output and also what
> >> your hardware and software environments are to help you.
> >> Certainly sounds like you ran out of memory though
> >>
> >> Cheers
> >> Bruce
> >>
> >> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon
> >>  >> > wrote:
> >> >
> >> > Ehsan
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> 
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> 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.
> >>
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> 
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 

Re: [Freesurfer] cannot allocate memory

[Douglas N Greve]

The problem is not the command, it is the size of the data it generates. 
You can try reducing the size of the anatomical to a bounding box around 
the brain. This is a bit tricky as you also have to compute a new 
registration. I can help step you through the process if you want to go 
in that direction.

On 03/22/2016 11:50 AM, Ehsan Tadayon wrote:
> Hi Doug,
>
> Thanks for your response. What I'm trying to do is to get each voxel's 
> times course in structural space and I was under the impression that 
> mri_vol2vol --mov func.nii would be the right way to go. Would you 
> please let me know what the best way would be to do this?
>
> best,
> Ehsan,.
>
>
> On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve 
> > wrote:
>
> that's going to create a pretty big volume as it will map your
> functional time course to a 256^3 float volume. If you have 100
> time points, then that will be about 7G.
>
> On 3/16/16 3:27 PM, Ehsan Tadayon wrote:
>> Hi Bruce,
>>
>> Thanks for your response. I'm using :
>>
>> freesurfer version:
>> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite
>> 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using:
>>
>> mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
>> func.anat.nii.gz
>>
>> Thanks in advance for your help.
>>
>> best regards,
>> Ehsan.
>>
>>
>>
>>
>> On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl
>> >
>> wrote:
>>
>> Hi Ehsan
>>
>> We need the full command line and screen output and also what
>> your hardware and software environments are to help you.
>> Certainly sounds like you ran out of memory though
>>
>> Cheers
>> Bruce
>>
>> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon
>> > > wrote:
>> >
>> > Ehsan
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Hi Doug,

Thanks for your response. What I'm trying to do is to get each voxel's
times course in structural space and I was under the impression that
mri_vol2vol --mov func.nii would be the right way to go. Would you please
let me know what the best way would be to do this?

best,
Ehsan,.


On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve 
wrote:

> that's going to create a pretty big volume as it will map your functional
> time course to a 256^3 float volume. If you have 100 time points, then that
> will be about 7G.
>
> On 3/16/16 3:27 PM, Ehsan Tadayon wrote:
>
> Hi Bruce,
>
> Thanks for your response. I'm using :
>
> freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS
> X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm
> using:
>
> mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
> func.anat.nii.gz
>
> Thanks in advance for your help.
>
> best regards,
> Ehsan.
>
>
>
>
> On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl  > wrote:
>
>> Hi Ehsan
>>
>> We need the full command line and screen output and also what your
>> hardware and software environments are to help you. Certainly sounds like
>> you ran out of memory though
>>
>> Cheers
>> Bruce
>>
>> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon <
>> ehsan.tadayo...@gmail.com> wrote:
>> >
>> > Ehsan
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory

[Douglas Greve]

that's going to create a pretty big volume as it will map your 
functional time course to a 256^3 float volume. If you have 100 time 
points, then that will be about 7G.


On 3/16/16 3:27 PM, Ehsan Tadayon wrote:

Hi Bruce,

Thanks for your response. I'm using :

freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 
on OS X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command 
that I'm using:


mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o 
func.anat.nii.gz


Thanks in advance for your help.

best regards,
Ehsan.




On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl 
> wrote:


Hi Ehsan

We need the full command line and screen output and also what your
hardware and software environments are to help you. Certainly
sounds like you ran out of memory though

Cheers
Bruce

> On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon
> wrote:
>
> Ehsan

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Hi Bruce,

Thanks for your response. I'm using :

freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS
X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm
using:

mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
func.anat.nii.gz

Thanks in advance for your help.

best regards,
Ehsan.




On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl 
wrote:

> Hi Ehsan
>
> We need the full command line and screen output and also what your
> hardware and software environments are to help you. Certainly sounds like
> you ran out of memory though
>
> Cheers
> Bruce
>
> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon 
> wrote:
> >
> > Ehsan
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory

[Bruce Fischl]

Hi Ehsan

We need the full command line and screen output and also what your hardware and 
software environments are to help you. Certainly sounds like you ran out of 
memory though

Cheers
Bruce

> On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon  wrote:
> 
> Ehsan

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

[Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Dear Freesurfer experts,

I'm trying to run mri_vol2vol on a functional mri to resample it onto
orig.mgz. I get this error:

```
mri_vol2vol(98217,0xa0ce01d4) malloc: *** mach_vm_map(size=262144) failed
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13664th slice

Cannot allocate memory
```
I was wondering if you have any suggestions. Thanks in advance for your
time.

Best,
Ehsan.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

can you send us the recon-all.log?
On Tue, 13 May 2014, Mayer Kristina 
wrote:

 Dear Bruce,

 I was running:
 recon-all -autorecon2-cp, after adding control points.
 When I then look at the surfaces using tkmedit -surfs or inflated surfaces 
 using tksurfer, everything seems to fit and I can open every output I like.
 Also values for volumes seem reasonable.

 Thanks in advance.

 Best,
 Kristina
 
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce 
 Fischl [fis...@nmr.mgh.harvard.edu]
 Gesendet: Montag, 12. Mai 2014 15:44
 An: Freesurfer support list
 Betreff: Re: [Freesurfer] Cannot allocate memory

 Hi Kristina

 you need to give us more context. What command is running when you get
 that error?

 cheers
 Bruce

 On Mon, 12 May 2014, Mayer Kristina wrote:

 Hi there,

 I am using freesurfer on MRI data of children.
 In one dataset I have following error appearing, I did not find described 
 before.

 MRISalloc(41043678, 76): could not allocate faces
 Cannot allocate memory
 Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 
 2014 x86_64 x86_64 x86_64 GNU/Linux

 Waht do I have to check or edit manually?

 Thanks!

 Best,
 Kristina


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 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.



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Cannot allocate memory

[Mayer Kristina]

Hi there,

I am using freesurfer on MRI data of children.
In one dataset I have following error appearing, I did not find described 
before.

MRISalloc(41043678, 76): could not allocate faces
Cannot allocate memory
Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 
x86_64 x86_64 x86_64 GNU/Linux

Waht do I have to check or edit manually?

Thanks!

Best,
Kristina


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory

[Bruce Fischl]

Hi Kristina

you need to give us more context. What command is running when you get 
that error?

cheers
Bruce

On Mon, 12 May 2014, Mayer Kristina wrote:

 Hi there,

 I am using freesurfer on MRI data of children.
 In one dataset I have following error appearing, I did not find described 
 before.

 MRISalloc(41043678, 76): could not allocate faces
 Cannot allocate memory
 Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 
 x86_64 x86_64 x86_64 GNU/Linux

 Waht do I have to check or edit manually?

 Thanks!

 Best,
 Kristina


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory

[Mayer Kristina]

Dear Bruce,

I was running:
recon-all -autorecon2-cp, after adding control points.
When I then look at the surfaces using tkmedit -surfs or inflated surfaces 
using tksurfer, everything seems to fit and I can open every output I like.
Also values for volumes seem reasonable.

Thanks in advance.

Best,
Kristina

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 12. Mai 2014 15:44
An: Freesurfer support list
Betreff: Re: [Freesurfer] Cannot allocate memory

Hi Kristina

you need to give us more context. What command is running when you get
that error?

cheers
Bruce

On Mon, 12 May 2014, Mayer Kristina wrote:

 Hi there,

 I am using freesurfer on MRI data of children.
 In one dataset I have following error appearing, I did not find described 
 before.

 MRISalloc(41043678, 76): could not allocate faces
 Cannot allocate memory
 Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 
 x86_64 x86_64 x86_64 GNU/Linux

 Waht do I have to check or edit manually?

 Thanks!

 Best,
 Kristina


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cannot allocate memory issue

[Borzello, Mia]

How do I check this? (Apologies for my ignorance.) So I might need to just use 
a different set of dicoms then?

thanks, 
Mia

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 1:02 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cannot allocate memory issue

It looks like there is too huge a topology error for it to continue:

CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
Excessive topologic defect encountered: could not allocate -729782272
edges for retessellation
Cannot allocate memory

I would suggested looking at the filled.mgz to make sure skull and/or
cerebellum are not included.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't running 
 to completion. I've attached the log file (recon-all.log), but it's unclear 
 to me what I should do to fix this problem. I tried to compute the lh.pial, 
 but I guess it was never made in the recon.

 Thanks so much,
 Mia


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Allison Stevens Player]

You can do:
tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

When you downloaded FreeSurfer, you would have also received the subject 
bert who is a good example to compare to. He will likely be located in:
$FREESURFER_HOME/subjects/bert

If you do the same command above for bert:
tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

You'll see what the filled.mgz should look like.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't running 
 to completion. I've attached the log file (recon-all.log), but it's unclear 
 to me what I should do to fix this problem. I tried to compute the lh.pial, 
 but I guess it was never made in the recon.

 Thanks so much,
 Mia




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Borzello, Mia]

It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
image, it doesn't look like the skull is present, but it does look like the 
cerebellum is.

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 1:28 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot allocate memory issue

You can do:
tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

When you downloaded FreeSurfer, you would have also received the subject
bert who is a good example to compare to. He will likely be located in:
$FREESURFER_HOME/subjects/bert

If you do the same command above for bert:
tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

You'll see what the filled.mgz should look like.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't running 
 to completion. I've attached the log file (recon-all.log), but it's unclear 
 to me what I should do to fix this problem. I tried to compute the lh.pial, 
 but I guess it was never made in the recon.

 Thanks so much,
 Mia





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Borzello, Mia]

would it be worth it at this point, to use another set of dicoms?
thanks, 
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
Sent: Monday, May 14, 2012 1:37 PM
To: Allison Stevens Player
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cannot allocate memory issue

It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
image, it doesn't look like the skull is present, but it does look like the 
cerebellum is.

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 1:28 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot allocate memory issue

You can do:
tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

When you downloaded FreeSurfer, you would have also received the subject
bert who is a good example to compare to. He will likely be located in:
$FREESURFER_HOME/subjects/bert

If you do the same command above for bert:
tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

You'll see what the filled.mgz should look like.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't running 
 to completion. I've attached the log file (recon-all.log), but it's unclear 
 to me what I should do to fix this problem. I tried to compute the lh.pial, 
 but I guess it was never made in the recon.

 Thanks so much,
 Mia





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Allison Stevens Player]

If you happen to have another MPRAGE for this subject, sure, you can try 
it.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

 would it be worth it at this point, to use another set of dicoms?
 thanks,
 m
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia
 Sent: Monday, May 14, 2012 1:37 PM
 To: Allison Stevens Player
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
 image, it doesn't look like the skull is present, but it does look like the 
 cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't running 
 to completion. I've attached the log file (recon-all.log), but it's unclear 
 to me what I should do to fix this problem. I tried to compute the lh.pial, 
 but I guess it was never made in the recon.

 Thanks so much,
 Mia





 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Allison Stevens Player]

Hi Mia,
You may want to check your talairach to make sure that looks okay. If 
that's not causing the problem, you can edit the wm.mgz to remove the 
cerebellum and then rerun and this should fix the problem.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
 image, it doesn't look like the skull is present, but it does look like the 
 cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't running 
 to completion. I've attached the log file (recon-all.log), but it's unclear 
 to me what I should do to fix this problem. I tried to compute the lh.pial, 
 but I guess it was never made in the recon.

 Thanks so much,
 Mia







___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Borzello, Mia]

Hey Allison, 

Thanks for you help. What do you mean by check your talairach? I'll hold off on 
using a different set of dicoms, and make that my last resort since it takes a 
day to complete. 
Thanks, 
m

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:16 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot allocate memory issue

Hi Mia,
You may want to check your talairach to make sure that looks okay. If
that's not causing the problem, you can edit the wm.mgz to remove the
cerebellum and then rerun and this should fix the problem.
Allison

On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
 image, it doesn't look like the skull is present, but it does look like the 
 cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't running 
 to completion. I've attached the log file (recon-all.log), but it's unclear 
 to me what I should do to fix this problem. I tried to compute the lh.pial, 
 but I guess it was never made in the recon.

 Thanks so much,
 Mia








___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Allison Stevens Player]

There are instructions on how to check it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

On Mon, 14 May 2012, Borzello, Mia wrote:

 Hey Allison,

 Thanks for you help. What do you mean by check your talairach? I'll hold off 
 on using a different set of dicoms, and make that my last resort since it 
 takes a day to complete.
 Thanks,
 m
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:16 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 Hi Mia,
 You may want to check your talairach to make sure that looks okay. If
 that's not causing the problem, you can edit the wm.mgz to remove the
 cerebellum and then rerun and this should fix the problem.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
 image, it doesn't look like the skull is present, but it does look like the 
 cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't 
 running to completion. I've attached the log file (recon-all.log), but 
 it's unclear to me what I should do to fix this problem. I tried to 
 compute the lh.pial, but I guess it was never made in the recon.

 Thanks so much,
 Mia










___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Bruce Fischl]

Hi Mia

can you clarify what you mean by a different set of dicoms? Did you 
acquire more than 1 T1-weighted structural on this subject? And can you 
send us an image of the acquisition, say in coronal view?

thanks
Bruce


On Mon, 14 May 
2012, Borzello, Mia wrote:

 Hey Allison,

 Thanks for you help. What do you mean by check your talairach? I'll hold off 
 on using a different set of dicoms, and make that my last resort since it 
 takes a day to complete.
 Thanks,
 m
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:16 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 Hi Mia,
 You may want to check your talairach to make sure that looks okay. If
 that's not causing the problem, you can edit the wm.mgz to remove the
 cerebellum and then rerun and this should fix the problem.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the popup 
 image, it doesn't look like the skull is present, but it does look like the 
 cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't 
 running to completion. I've attached the log file (recon-all.log), but 
 it's unclear to me what I should do to fix this problem. I tried to 
 compute the lh.pial, but I guess it was never made in the recon.

 Thanks so much,
 Mia








 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Bruce Fischl]

actually I wanted one from tkmedit. Can you tell us something about the 
acquisition? What kind of scan is it? What resolution? And if you can 
send us images from tkmedit in coronal and sagittal view that would help 
too (say of the orig.mgz)

Bruce
On Mon, 14 May 2012, Borzello, Mia wrote:

 I have two sets of dicoms: one is an axial view, while the other is coronal 
 (this is the one i was using). I attached a screenshot. I'm not sure if 
 that's what you wanted? 

 thanks
 mia
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:32 PM
 To: Borzello, Mia
 Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 Hi Mia

 can you clarify what you mean by a different set of dicoms? Did you
 acquire more than 1 T1-weighted structural on this subject? And can you
 send us an image of the acquisition, say in coronal view?

 thanks
 Bruce


 On Mon, 14 May
 2012, Borzello, Mia wrote:

 Hey Allison,

 Thanks for you help. What do you mean by check your talairach? I'll hold off 
 on using a different set of dicoms, and make that my last resort since it 
 takes a day to complete.
 Thanks,
 m
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:16 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 Hi Mia,
 You may want to check your talairach to make sure that looks okay. If
 that's not causing the problem, you can edit the wm.mgz to remove the
 cerebellum and then rerun and this should fix the problem.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
 popup image, it doesn't look like the skull is present, but it does look 
 like the cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't 
 running to completion. I've attached the log file (recon-all.log), but 
 it's unclear to me what I should do to fix this problem. I tried to 
 compute the lh.pial, but I guess it was never made in the recon.

 Thanks so much,
 Mia








 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Borzello, Mia]

so that's most likely the problem?

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:46 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot allocate memory issue

actually I wanted one from tkmedit. Can you tell us something about the
acquisition? What kind of scan is it? What resolution? And if you can
send us images from tkmedit in coronal and sagittal view that would help
too (say of the orig.mgz)

Bruce
On Mon, 14 May 2012, Borzello, Mia wrote:

 I have two sets of dicoms: one is an axial view, while the other is coronal 
 (this is the one i was using). I attached a screenshot. I'm not sure if 
 that's what you wanted?

 thanks
 mia
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:32 PM
 To: Borzello, Mia
 Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 Hi Mia

 can you clarify what you mean by a different set of dicoms? Did you
 acquire more than 1 T1-weighted structural on this subject? And can you
 send us an image of the acquisition, say in coronal view?

 thanks
 Bruce


 On Mon, 14 May
 2012, Borzello, Mia wrote:

 Hey Allison,

 Thanks for you help. What do you mean by check your talairach? I'll hold off 
 on using a different set of dicoms, and make that my last resort since it 
 takes a day to complete.
 Thanks,
 m
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:16 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 Hi Mia,
 You may want to check your talairach to make sure that looks okay. If
 that's not causing the problem, you can edit the wm.mgz to remove the
 cerebellum and then rerun and this should fix the problem.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
 popup image, it doesn't look like the skull is present, but it does look 
 like the cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't 
 running to completion. I've attached the log file (recon-all.log), but 
 it's unclear to me what I should do to fix this problem. I tried to 
 compute the lh.pial, but I guess it was never made in the recon.

 Thanks so much,
 Mia








 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Borzello, Mia]

oh woops. sorry. 
so both of these sets of dicoms are T2

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:46 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot allocate memory issue

actually I wanted one from tkmedit. Can you tell us something about the
acquisition? What kind of scan is it? What resolution? And if you can
send us images from tkmedit in coronal and sagittal view that would help
too (say of the orig.mgz)

Bruce
On Mon, 14 May 2012, Borzello, Mia wrote:

 I have two sets of dicoms: one is an axial view, while the other is coronal 
 (this is the one i was using). I attached a screenshot. I'm not sure if 
 that's what you wanted?

 thanks
 mia
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:32 PM
 To: Borzello, Mia
 Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 Hi Mia

 can you clarify what you mean by a different set of dicoms? Did you
 acquire more than 1 T1-weighted structural on this subject? And can you
 send us an image of the acquisition, say in coronal view?

 thanks
 Bruce


 On Mon, 14 May
 2012, Borzello, Mia wrote:

 Hey Allison,

 Thanks for you help. What do you mean by check your talairach? I'll hold off 
 on using a different set of dicoms, and make that my last resort since it 
 takes a day to complete.
 Thanks,
 m
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:16 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 Hi Mia,
 You may want to check your talairach to make sure that looks okay. If
 that's not causing the problem, you can edit the wm.mgz to remove the
 cerebellum and then rerun and this should fix the problem.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
 popup image, it doesn't look like the skull is present, but it does look 
 like the cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to just 
 use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't 
 running to completion. I've attached the log file (recon-all.log), but 
 it's unclear to me what I should do to fix this problem. I tried to 
 compute the lh.pial, but I guess it was never made in the recon.

 Thanks so much,
 Mia








 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] cannot allocate memory issue

[Bruce Fischl]

yes, that's the kind of thing I was worried about. You need a relatively 
high resolution set of T1s (mprage, FLASH/SPGR, close to 1mm isotropic).

On Mon, 14 May 2012, 
Borzello, Mia wrote:

 oh woops. sorry.
 so both of these sets of dicoms are T2
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:46 PM
 To: Borzello, Mia
 Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 actually I wanted one from tkmedit. Can you tell us something about the
 acquisition? What kind of scan is it? What resolution? And if you can
 send us images from tkmedit in coronal and sagittal view that would help
 too (say of the orig.mgz)

 Bruce
 On Mon, 14 May 2012, Borzello, Mia wrote:

 I have two sets of dicoms: one is an axial view, while the other is coronal 
 (this is the one i was using). I attached a screenshot. I'm not sure if 
 that's what you wanted?

 thanks
 mia
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:32 PM
 To: Borzello, Mia
 Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 Hi Mia

 can you clarify what you mean by a different set of dicoms? Did you
 acquire more than 1 T1-weighted structural on this subject? And can you
 send us an image of the acquisition, say in coronal view?

 thanks
 Bruce


 On Mon, 14 May
 2012, Borzello, Mia wrote:

 Hey Allison,

 Thanks for you help. What do you mean by check your talairach? I'll hold 
 off on using a different set of dicoms, and make that my last resort since 
 it takes a day to complete.
 Thanks,
 m
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:16 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 Hi Mia,
 You may want to check your talairach to make sure that looks okay. If
 that's not causing the problem, you can edit the wm.mgz to remove the
 cerebellum and then rerun and this should fix the problem.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
 popup image, it doesn't look like the skull is present, but it does look 
 like the cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to 
 just use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't 
 running to completion. I've attached the log file (recon-all.log), but 
 it's unclear to me what I should do to fix this problem. I tried to 
 compute the lh.pial, but I guess it was never made in the recon.

 Thanks so much,
 Mia








 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] cannot allocate memory issue

[Borzello, Mia]

okay, well i'll give it a try with a set of T1s. Thanks guys!

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, May 14, 2012 3:57 PM
To: Borzello, Mia
Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] cannot allocate memory issue

yes, that's the kind of thing I was worried about. You need a relatively
high resolution set of T1s (mprage, FLASH/SPGR, close to 1mm isotropic).

On Mon, 14 May 2012,
Borzello, Mia wrote:

 oh woops. sorry.
 so both of these sets of dicoms are T2
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:46 PM
 To: Borzello, Mia
 Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 actually I wanted one from tkmedit. Can you tell us something about the
 acquisition? What kind of scan is it? What resolution? And if you can
 send us images from tkmedit in coronal and sagittal view that would help
 too (say of the orig.mgz)

 Bruce
 On Mon, 14 May 2012, Borzello, Mia wrote:

 I have two sets of dicoms: one is an axial view, while the other is coronal 
 (this is the one i was using). I attached a screenshot. I'm not sure if 
 that's what you wanted?

 thanks
 mia
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:32 PM
 To: Borzello, Mia
 Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 Hi Mia

 can you clarify what you mean by a different set of dicoms? Did you
 acquire more than 1 T1-weighted structural on this subject? And can you
 send us an image of the acquisition, say in coronal view?

 thanks
 Bruce


 On Mon, 14 May
 2012, Borzello, Mia wrote:

 Hey Allison,

 Thanks for you help. What do you mean by check your talairach? I'll hold 
 off on using a different set of dicoms, and make that my last resort since 
 it takes a day to complete.
 Thanks,
 m
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 3:16 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 Hi Mia,
 You may want to check your talairach to make sure that looks okay. If
 that's not causing the problem, you can edit the wm.mgz to remove the
 cerebellum and then rerun and this should fix the problem.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 It says that it couldn't open rh.orig.nofix and  lh.orig.nofix. On the 
 popup image, it doesn't look like the skull is present, but it does look 
 like the cerebellum is.
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:28 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: RE: [Freesurfer] cannot allocate memory issue

 You can do:
 tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 When you downloaded FreeSurfer, you would have also received the subject
 bert who is a good example to compare to. He will likely be located in:
 $FREESURFER_HOME/subjects/bert

 If you do the same command above for bert:
 tkmedit bert filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix

 You'll see what the filled.mgz should look like.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 How do I check this? (Apologies for my ignorance.) So I might need to 
 just use a different set of dicoms then?

 thanks,
 Mia
 
 From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu]
 Sent: Monday, May 14, 2012 1:02 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] cannot allocate memory issue

 It looks like there is too huge a topology error for it to continue:

 CORRECTING DEFECT 23 (vertices=143258, convex hull=19937)
 Excessive topologic defect encountered: could not allocate -729782272
 edges for retessellation
 Cannot allocate memory

 I would suggested looking at the filled.mgz to make sure skull and/or
 cerebellum are not included.
 Allison

 On Mon, 14 May 2012, Borzello, Mia wrote:

 Hi all,

 I was wondering if you could help me figure out why the recon isn't 
 running to completion. I've attached the log file (recon-all.log), but 
 it's unclear to me what I should do to fix this problem. I tried to 
 compute the lh.pial, but I guess it was never made in the recon.

 Thanks so much,
 Mia








 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer







___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom

[Freesurfer] Cannot allocate memory

[Pradeep]

Hello All,

I get the following error while running mri_glmfit. I am using freesurfer
V5.0. But qdce seem to run well with the similar settings.

-log---

[pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd
g2v0.fsgd --C group.diff.mtx
gdfReadHeader: reading g2v0.fsgd
INFO: gd2mtx_method is dods

$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
cwd /data/rawdata/API/FS_MPRAGE/fsgd
cmdline mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C
group.diff.mtx
sysname  Linux
hostname
machine  x86_64
user pthiyyagura
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
logyflag 0
usedti  0
FSGD g2v0.fsgd
glmdir g2v0
IllCondOK 0
DoFFx 0
Creating output directory g2v0
Loading y from /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
MRIalloc: could not allocate 1378828612 slices

Cannot allocate memory

end---

Any suggestion on this would be greatly appreciated.

Thanks,
Pradeep
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cannot allocate memory

[Douglas Greve]

 How was fsgd_input.mgh created? What do you get when you run:
mri_info fsgd_input.mgh

On 10/14/10 7:53 PM, Pradeep wrote:

Hello All,

I get the following error while running mri_glmfit. I am using 
freesurfer V5.0. But qdce seem to run well with the similar settings.


-log---

[pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh 
--fsgd g2v0.fsgd --C group.diff.mtx

gdfReadHeader: reading g2v0.fsgd
INFO: gd2mtx_method is dods

$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $
cwd /data/rawdata/API/FS_MPRAGE/fsgd
cmdline mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd 
--C group.diff.mtx

sysname  Linux
hostname
machine  x86_64
user pthiyyagura
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
logyflag 0
usedti  0
FSGD g2v0.fsgd
glmdir g2v0
IllCondOK 0
DoFFx 0
Creating output directory g2v0
Loading y from /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh
MRIalloc: could not allocate 1378828612 slices

Cannot allocate memory

end---

Any suggestion on this would be greatly appreciated.

Thanks,
Pradeep


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

RES: [Freesurfer] Cannot allocate memory / can't allocate region

[ppj]

Check ulimit -m 

That's the max mem per process.

ulimit -m 0 

Maybe will help.

-- Pedro Paulo Jr 
E71 Nokia
-Msg original-
De: Jürgen Hänggi
Enviada:  01/07/2009 02:36:36
Para: Freesurfer Mailinglist
Assunto:  [Freesurfer] Cannot allocate memory / can't allocate region

Dear FS experts

I am using high resolution (0.75x0.75x0.75 mm) data within FS but the
following error occurred:

...
vertex spacing 0.69 +- 0.21 (0.00--6.06) (max @ vno 265258 -- 114262)
face area 0.19 +- 0.10 (0.00--4.49)
mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice

000: dt: 0., sse=4822516.5, rms=2.25
rms = 2.94, time step reduction 1 of 3 to 0.250...
043: dt: 0.2500, sse=4898456.5, rms=1.89
rms = 1.86, time step reduction 2 of 3 to 0.125...
044: dt: 0.2500, sse=5293477.5, rms=1.86
045: dt: 0.1250, sse=5277681.5, rms=1.76
046: dt: 0.1250, sse=5237215.5, rms=1.70
rms = 1.69, time step reduction 3 of 3 to 0.062...
047: dt: 0.1250, sse=5270459.0, rms=1.69
positioning took 16.1 minutes
inhibiting deformation at non-cortical midline structures...
correcting aseg with surfaces...
Cannot allocate memory
Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue
Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386

recon-all exited with ERRORS at Wed Jul  1 04:20:34 CEST 2009

[juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri]

I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors
8192

The process terminated before all RAM is active and no swap is used.

Any idea?

Thanks in advance
Regards
Jürgen


Juergen Haenggi
Ph.D. (Dr. des.)
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Cannot allocate memory / can't allocate region

[Bruce Fischl]

Hi Juergen,

how much ram do you have in the machine?

Bruce
On Wed, 1 Jul 2009, Jürgen Hänggi 
wrote:



Dear FS experts

I am using high resolution (0.75x0.75x0.75 mm) data within FS but the
following error occurred:

...
vertex spacing 0.69 +- 0.21 (0.00--6.06) (max @ vno 265258 -- 114262)
face area 0.19 +- 0.10 (0.00--4.49)
mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice

000: dt: 0., sse=4822516.5, rms=2.25
rms = 2.94, time step reduction 1 of 3 to 0.250...
043: dt: 0.2500, sse=4898456.5, rms=1.89
rms = 1.86, time step reduction 2 of 3 to 0.125...
044: dt: 0.2500, sse=5293477.5, rms=1.86
045: dt: 0.1250, sse=5277681.5, rms=1.76
046: dt: 0.1250, sse=5237215.5, rms=1.70
rms = 1.69, time step reduction 3 of 3 to 0.062...
047: dt: 0.1250, sse=5270459.0, rms=1.69
positioning took 16.1 minutes
inhibiting deformation at non-cortical midline structures...
correcting aseg with surfaces...
Cannot allocate memory
Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue
Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386

recon-all exited with ERRORS at Wed Jul  1 04:20:34 CEST 2009

[juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri]

I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors
8192

The process terminated before all RAM is active and no swap is used.

Any idea?

Thanks in advance
Regards
Jürgen


Juergen Haenggi
Ph.D. (Dr. des.)
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Cannot allocate memory / can't allocate region

[Jürgen Hänggi]

Dear FS experts

I am using high resolution (0.75x0.75x0.75 mm) data within FS but the
following error occurred:

...
vertex spacing 0.69 +- 0.21 (0.00--6.06) (max @ vno 265258 -- 114262)
face area 0.19 +- 0.10 (0.00--4.49)
mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice

000: dt: 0., sse=4822516.5, rms=2.25
rms = 2.94, time step reduction 1 of 3 to 0.250...
043: dt: 0.2500, sse=4898456.5, rms=1.89
rms = 1.86, time step reduction 2 of 3 to 0.125...
044: dt: 0.2500, sse=5293477.5, rms=1.86
045: dt: 0.1250, sse=5277681.5, rms=1.76
046: dt: 0.1250, sse=5237215.5, rms=1.70
rms = 1.69, time step reduction 3 of 3 to 0.062...
047: dt: 0.1250, sse=5270459.0, rms=1.69
positioning took 16.1 minutes
inhibiting deformation at non-cortical midline structures...
correcting aseg with surfaces...
Cannot allocate memory
Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue
Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386

recon-all exited with ERRORS at Wed Jul  1 04:20:34 CEST 2009

[juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri]

I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors
8192

The process terminated before all RAM is active and no swap is used.

Any idea?

Thanks in advance
Regards
Jürgen


Juergen Haenggi
Ph.D. (Dr. des.)
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Cannot allocate memory

[Jürgen Hänggi]

Dear FS experts

I tried to make an average subject of 52 subjects, but it seems that an
already fixed error is back:

Checking 47 
/usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
laris_Male_48.mgh
Checking 48 
/usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
laris_Male_49.mgh
Checking 49 
/usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
laris_Male_50.mgh
Checking 50 
/usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
laris_Male_51.mgh
Checking 51 
/usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
laris_Male_52.mgh
nframestot = 52
Allocing output
MRIalloc(256, 256, 256): could not allocate 262144 bytes for 11862th slice

Cannot allocate memory
ERROR: make_average_volume
[neuropsy...@130 subjects]$


I had the same problem with an older Mac FS version. Is there also a fixed
version of FS 4.2.0 for Linux CENTOS 32 bit?

Thanks in advance
Regards
Jürgen


Juergen Haenggi
Ph.D. (Dr. des.)
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Cannot allocate memory

[Nick Schmansky]

Juergen,

Are you running v4.2.0 of linux centos 32b, or asking if this problem
was fixed in that version?  ie., which version are you running now?  I'm
not aware of this problem currently (that is, I too thought it was fixed
some time ago).

Nick


On Fri, 2009-02-13 at 16:22 +0100, J=?ISO-8859-1?B?/A==?=rgen H=?
ISO-8859-1?B?5A==?=nggi wrote:
 Dear FS experts
 
 I tried to make an average subject of 52 subjects, but it seems that an
 already fixed error is back:
 
 Checking 47 
 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
 laris_Male_48.mgh
 Checking 48 
 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
 laris_Male_49.mgh
 Checking 49 
 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
 laris_Male_50.mgh
 Checking 50 
 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
 laris_Male_51.mgh
 Checking 51 
 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po
 laris_Male_52.mgh
 nframestot = 52
 Allocing output
 MRIalloc(256, 256, 256): could not allocate 262144 bytes for 11862th slice
 
 Cannot allocate memory
 ERROR: make_average_volume
 [neuropsy...@130 subjects]$
 
 
 I had the same problem with an older Mac FS version. Is there also a fixed
 version of FS 4.2.0 for Linux CENTOS 32 bit?
 
 Thanks in advance
 Regards
 Jürgen
 
 
 Juergen Haenggi
 Ph.D. (Dr. des.)
 Division Neuropsychology
 Institute of Psychology
 University of Zurich
 Binzmuehlestrasse 14, PO Box 25
 8050 Zurich, Switzerland
 0041 44 635 73 97 (phone office)
 0041 76 445 86 84 (phone mobile)
 0041 44 635 74 09 (fax office)
 BIN 4.D.04 (office room number)
 j.haenggi[at]psychologie.uzh.ch (email)
 http://www.psychologie.uzh.ch/neuropsy/ (website)
 http://www.juergenhaenggi.ch (private website)
 
 This e-mail (and any attachment/s) contains confidential and/or privileged
 information. If you are not the intended recipient (or have received this
 e-mail in error) please notify the sender immediately and destroy this
 e-mail. Any unauthorised copying, disclosure or distribution of the
 material in this e-mail is strictly forbidden.
 
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cannot allocate memory problem when using make average subject

[Doug Greve]

I've put the files back in that location (make_average_*). Run 
make_average_subject with --no-aseg. But I'm not sure this is the 
problem. It looks like it is failing when creating the average surface 
(the fix above is for the volume only). But give it a try. Also, 
remember to send the entire log file so we can better debug it.


doug



Jiefeng Jiang wrote:


Hi,
 
I was trying to build an average subject using 250 subjects and I got 
the following error message:
 
processing subject nor76 (246 of 250)
reading spherical surface 
/DATA_FREESURFER/Data/nor76/surf/rh.sphere.reg...

reading colortable from annotation file...
colortable with 35 entries read (originally 
/space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)

curvature mean = -0.017, std = 0.597
curvature mean = -0.064, std = 0.640
ripping medial wall...
computing parameterization for surface 
/DATA_FREESURFER/Data/nor76/surf/rh.inflated.H...

ImageAlloc: could not allocate 512x256 buffer
 
curvature mean = -0.088, std = 0.872

Cannot allocate memory
I saw someone discussing this issue a few month ago and Doug 
provided new scripts of make_average_subject, make_average_volume and 
make_average_surface to solve this problem. However, I can't find 
these files using the link 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
Can anyone tell me whether and how this problem has been solved? 
Thanks in advance!
 
 
Jiefeng Jiang
 




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] cannot allocate memory problem when using make average subject

[Jiefeng Jiang]

Hi,

I was trying to build an average subject using 250 subjects and I got the 
following error message:

processing subject nor76 (246 of 250)
reading spherical surface /DATA_FREESURFER/Data/nor76/surf/rh.sphere.reg...
reading colortable from annotation file...
colortable with 35 entries read (originally 
/space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt)
curvature mean = -0.017, std = 0.597
curvature mean = -0.064, std = 0.640
ripping medial wall...
computing parameterization for surface 
/DATA_FREESURFER/Data/nor76/surf/rh.inflated.H...
ImageAlloc: could not allocate 512x256 buffer

curvature mean = -0.088, std = 0.872
Cannot allocate memory

I saw someone discussing this issue a few month ago and Doug provided new 
scripts of make_average_subject, make_average_volume and make_average_surface 
to solve this problem. However, I can't find these files using the link 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Can anyone tell me whether and how this problem has been solved? Thanks in 
advance!


Jiefeng Jiang
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer