Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Anna Daniels]

Hi Andrew, hi Bruce,

thanks for the tip! Unfortunately, the dev version of mri_normalize did not
work (resulted in the same error log) but simply manually checking the
control points in the respective cross runs and deleting the ones outside
the brain before rerunning worked!

Best,
Anna

2018-04-11 23:22 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:

> p.s. you probably want to grab a new freeview also, as it lets you jump to
> the voxel coords of each control point so you can see them
>
> On Wed, 11 Apr 2018, Hoopes, Andrew wrote:
>
>
>> Hi Anna,
>>
>>
>>
>> You can download the new mri_normalize from this link -
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_
>> binaries/centos6_x86_64/mri_normalize
>>
>>
>>
>> To get it into your FS installation, first set executable permissions and
>> then move it into your
>> $FREESURFER_HOME/bin directory (sudo might be required):
>>
>>
>>
>> chmod +x /path/to/downloaded/mri_normalize
>>
>> mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/
>>
>>
>>
>> best
>>
>> Andrew
>>
>>
>>
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels
>> <anna.dani...@fu-berlin.de>
>> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, April 9, 2018 at 1:10 PM
>> To: FS Help <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] recon-all: exited with errors (white matter
>> peak at 110, cannot allocate
>> memory)
>>
>>
>>
>> Hi Bruce,
>>
>> thank you for the quick reply!
>>
>> Ubuntu 16.04 LTS 64-bit
>>
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>
>> Please let me know how to incorporate the new version into the
>> installation.
>>
>> Thank you very much and best,
>>
>> Anna
>>
>>
>>
>> Hi Anna
>>
>> no attachments :<
>>
>> Srishti's issue stemmed from control points outside of the head. The
>> current (dev) version of mri_normalize detects and removes them. Can you
>> grab a new version of mri_normalize and see if it fixes your problem? Let
>> us know your hardware/software environment and we will get it to you
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 6 Apr 2018, Anna Daniels wrote:
>>
>> > Hi Bruce, hi Srishti,
>> >
>> > I have exactly the same problem with several subjects rerunning
>> recon-all
>> > and there was sufficient memory available. I also tried out the last
>> command
>> > directly which resulted in the same error log.
>> >
>> > ?mri_normalize -f/home/anna/FREESURFER/00_DAT
>> A_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
>> > uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
>> > aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>> >
>> > Attached you can find the input file.
>> >
>> > Thank you and best,
>> > Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
>>
>>
>>
>>
>
> 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
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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

p.s. you probably want to grab a new freeview also, as it lets you jump 
to the voxel coords of each control point so you can see them
On Wed, 11 Apr 
2018, Hoopes, Andrew wrote:




Hi Anna,

 

You can download the new mri_normalize from this link -
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize

 

To get it into your FS installation, first set executable permissions and then 
move it into your
$FREESURFER_HOME/bin directory (sudo might be required):

 

chmod +x /path/to/downloaded/mri_normalize

mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/

 

best

Andrew

 

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels 
<anna.dani...@fu-berlin.de>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate
memory)

 

Hi Bruce,

thank you for the quick reply!

Ubuntu 16.04 LTS 64-bit

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Please let me know how to incorporate the new version into the installation.

Thank you very much and best,

Anna



Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
-f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]


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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Hoopes, Andrew]

Hi Anna,

You can download the new mri_normalize from this link - 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_normalize

To get it into your FS installation, first set executable permissions and then 
move it into your $FREESURFER_HOME/bin directory (sudo might be required):

chmod +x /path/to/downloaded/mri_normalize
mv /path/to/downloaded/mri_normalize ${FREESURFER_HOME}/bin/

best
Andrew

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels 
<anna.dani...@fu-berlin.de>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Hoopes, Andrew]

The fix that Anna needs was committed last Friday.
Andrew

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Dicamillo, Robert" 
<rdicami...@mgh.harvard.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 10, 2018 at 12:27 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Dicamillo, Robert" <rdicami...@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

If you are running on Ubuntu, I have a build of the freesurfer source checked
out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system 
using gcc 4.9.

However,  I did not have the test data to run tests, so I must add the 
disclaimer that the binaries
have not gone thru the usual tests.  But if you want to try it, you can download
the compressed ~2G archive from the link below.  It is an archive of the 
./install
tree with ./bin, ./lib, etc.

https://drive.google.com/file/d/1hWs3gdfVExRMW5nl-aufQyMX8yWSHi8Y/view?usp=sharing

- rob

On Apr 9, 2018, at 2:31 PM, Hoopes, Andrew 
<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote:

Hi Anna,

Unfortunately, we’re not able to build the dev code right now due to a compile 
error, but this should get sorted out within the next day or two, so I can help 
you out with getting this new mri_normalize then

best
Andrew

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Anna Daniels 
<anna.dani...@fu-berlin.de<mailto:anna.dani...@fu-berlin.de>>
Reply-To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Dicamillo, Robert]

If you are running on Ubuntu, I have a build of the freesurfer source checked
out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system 
using gcc 4.9.

However,  I did not have the test data to run tests, so I must add the 
disclaimer that the binaries
have not gone thru the usual tests.  But if you want to try it, you can download
the compressed ~2G archive from the link below.  It is an archive of the 
./install
tree with ./bin, ./lib, etc.

https://drive.google.com/file/d/1hWs3gdfVExRMW5nl-aufQyMX8yWSHi8Y/view?usp=sharing

- rob

On Apr 9, 2018, at 2:31 PM, Hoopes, Andrew 
<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote:

Hi Anna,

Unfortunately, we’re not able to build the dev code right now due to a compile 
error, but this should get sorted out within the next day or two, so I can help 
you out with getting this new mri_normalize then

best
Andrew

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Anna Daniels 
<anna.dani...@fu-berlin.de<mailto:anna.dani...@fu-berlin.de>>
Reply-To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Hoopes, Andrew]

Hi Anna,

Unfortunately, we’re not able to build the dev code right now due to a compile 
error, but this should get sorted out within the next day or two, so I can help 
you out with getting this new mri_normalize then

best
Andrew

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels 
<anna.dani...@fu-berlin.de>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Anna Daniels]

Hi Bruce,

thank you for the quick reply!

Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Please let me know how to incorporate the new version into the installation.

Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last
command
> directly which resulted in the same error log.
>
> ?mri_normalize -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_
cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The 
current (dev) version of mri_normalize detects and removes them. Can you 
grab a new version of mri_normalize and see if it fixes your problem? Let 
us know your hardware/software environment and we will get it to you


cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:


Hi Bruce, hi Srishti,

I have exactly the same problem with several subjects rerunning recon-all
and there was sufficient memory available. I also tried out the last command
directly which resulted in the same error log.

 mri_normalize 
-f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz

Attached you can find the input file.

Thank you and best,
Anna​[icon_10_generic_list.png]  22275_T1_fs_edit.zip[IMAGE]




  ​can you email us the input file and the full command line you
  ran?
  On Thu, 5
  Apr 2018, srishti goel wrote:

  > So it gave this error:
  >
  > 3d normalization pass 1 of 2
  >
  > white matter peak found at 110
  >
  > HISTOalloc(-2147483648): could not allocate histogram
  >
  > Cannot allocate memory
  >
  >
  > Best,
  > Srishti
  > Social/Clinical Research Specialist
  > Child Imaging Research and Life Experiences Lab
  > University of North Carolina at Chapel Hill
  > email (W): srish...@email.unc.edu
  > skype: srishti.goel12
  >
  >
  > On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl
   wrote:
  >       let's see if it works. If it does, you should be able to
  run
  >
  >       recon-all -s SUBJID -make all
  >
  >       cheers
  >       Bruce
  >
  >
  >       On Thu, 5 Apr 2018, srishti goel wrote:
  >
  >             Should I re-run the recon-all after running the
  last command from recon-all.cmd?
  >
  >             Best,
  >             Srishti
  >             Social/Clinical Research Specialist
  >             Child Imaging Research and Life Experiences Lab
  >             University of North Carolina at Chapel Hill
  >             email (W): srish...@email.unc.edu
  >             skype: srishti.goel12
  >
  >
  >             On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl
   wrote:
  >             ? ? ? Hi Srishti
  >
  >             ? ? ? if you look in the subject's scripts dir
  there should be a file named "recon-all.cmd". Try
  >             rerunning the last
  >             ? ? ? command in it (probably from the mri dir)
  >
  >             ? ? ? cheers
  >             ? ? ? Bruce
  >             ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
  >
  >             ? ? ? ? ? ? I am sorry, I am not sure what do you
  mean by running the command line directly?
  >             ? ? ? ? ? ? I use the following command:
  >
  >             ? ? ? ? ? ? sbatch --mem 2200 -t 6-00:00
  --mail-type END --mail-user srish...@email.unc.edu --wrap
  >             "export
  >             ? ? ? ? ? ?
  SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
  recon-all -s 13166
  >             ? ? ? ? ? ? -autorecon2-cp -autorecon3 -nowmsa"
  >
  >
  >             ? ? ? ? ? ? where sbatch. until export is our
  local server submission command and I run this
  >             command from the
  >             ? ? ? ? ? ? command line itself, not
  >             ? ? ? ? ? ? using any script.
  >
  >
  >             ? ? ? ? ? ? Best,
  >             ? ? ? ? ? ? Srishti
  >             ? ? ? ? ? ? Social/Clinical Research Specialist
  >             ? ? ? ? ? ? Child Imaging Research and Life
  Experiences Lab
  >             ? ? ? ? ? ? University of North Carolina at Chapel
  Hill
  >             ? ? ? ? ? ? email (W): srish...@email.unc.edu
  >             ? ? ? ? ? ? skype: srishti.goel12
  >
  >
  >             ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:24 PM, Bruce
  Fischl  wrote:
  >             ? ? ? ? ? ? ? ? ? if you run the command that
  failed again on the command line directly (that is, not
  >             in
  >             ? ? ? ? ? ? recon-all) does it fail
  >             ? ? ? ? ? ? ? ? ? again?
  >
  >             ? ? ? ? ? ? ? ? ? On Thu, 5 Apr 2018, srishti goel
  wrote:
  >
  >             ? ? ? ? ? ? ? ? ? ? ? ? Hi Bruce,
  >
  >             ? ? ? ? ? ? ? ? ? ? ? ? The machine definitely
  hasn't run out of memory. Here is the memory usage
  >             ? ? ? ? ? ? ? ? ? ? ? ? from recon-all.log ?
  >
  >             ? ? ? ? ? ? 

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Anna Daniels]

Hi Bruce, hi Srishti,

I have exactly the same problem with several subjects rerunning recon-all
and there was sufficient memory available. I also tried out the last
command directly which resulted in the same error log.

 mri_normalize -f /home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_
edits_transfer/rreruncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat
-mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz

Attached you can find the input file.

Thank you and best,
Anna​
 22275_T1_fs_edit.zip

​



> can you email us the input file and the full command line you ran?
> On Thu, 5
> Apr 2018, srishti goel wrote:
>
> > So it gave this error:
> >
> > 3d normalization pass 1 of 2
> >
> > white matter peak found at 110
> >
> > HISTOalloc(-2147483648): could not allocate histogram
> >
> > Cannot allocate memory
> >
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
> > skype: srishti.goel12
> >
> >
> > On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   let's see if it works. If it does, you should be able to run
> >
> >   recon-all -s SUBJID -make all
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > Should I re-run the recon-all after running the last command
> from recon-all.cmd?
> >
> > Best,
> > Srishti
> > Social/Clinical Research Specialist
> > Child Imaging Research and Life Experiences Lab
> > University of North Carolina at Chapel Hill
> > email (W): srish...@email.unc.edu
> > skype: srishti.goel12
> >
> >
> > On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> > ? ? ? Hi Srishti
> >
> > ? ? ? if you look in the subject's scripts dir there should
> be a file named "recon-all.cmd". Try
> > rerunning the last
> > ? ? ? command in it (probably from the mri dir)
> >
> > ? ? ? cheers
> > ? ? ? Bruce
> > ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > ? ? ? ? ? ? I am sorry, I am not sure what do you mean by
> running the command line directly?
> > ? ? ? ? ? ? I use the following command:
> >
> > ? ? ? ? ? ? sbatch --mem 2200 -t 6-00:00 --mail-type END
> --mail-user srish...@email.unc.edu --wrap
> > "export
> > ? ? ? ? ? ? SUBJECTS_DIR=/proj/hng/sherida
> nlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 13166
> > ? ? ? ? ? ? -autorecon2-cp -autorecon3 -nowmsa"
> >
> >
> > ? ? ? ? ? ? where sbatch. until export is our local
> server submission command and I run this
> > command from the
> > ? ? ? ? ? ? command line itself, not
> > ? ? ? ? ? ? using any script.
> >
> >
> > ? ? ? ? ? ? Best,
> > ? ? ? ? ? ? Srishti
> > ? ? ? ? ? ? Social/Clinical Research Specialist
> > ? ? ? ? ? ? Child Imaging Research and Life Experiences Lab
> > ? ? ? ? ? ? University of North Carolina at Chapel Hill
> > ? ? ? ? ? ? email (W): srish...@email.unc.edu
> > ? ? ? ? ? ? skype: srishti.goel12
> >
> >
> > ? ? ? ? ? ? On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> > ? ? ? ? ? ? ? ? ? if you run the command that failed again
> on the command line directly (that is, not
> > in
> > ? ? ? ? ? ? recon-all) does it fail
> > ? ? ? ? ? ? ? ? ? again?
> >
> > ? ? ? ? ? ? ? ? ? On Thu, 5 Apr 2018, srishti goel wrote:
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? Hi Bruce,
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? The machine definitely hasn't run
> out of memory. Here is the memory usage
> > ? ? ? ? ? ? ? ? ? ? ? ? from recon-all.log ?
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?total ? ? ? ? ?
> ? ?used ? ? ? ?free ? ? ? ? ? ? ? ? ?
> > ? ? ? ? ? ? ? ? ? ? ? ? shared ?buff/cache ? available
> > ? ? ? ? ? ? ? ? ? ? ? ? Mem: ? ? ?263726968 ? ?34330048 ?
> 152102696 ? ? ? 12944 ? ?77294224 ?
> > ? ? ? ? ? ? ? ? ? ? ? ? 191963372
> > ? ? ? ? ? ? ? ? ? ? ? ? Swap: ? ? ? 2097148 ? ? ? ? ? 0 ? ?
> ? ? ? ? 2097148
> >
> >
> >
> >
> > ? ? ? ? ? ? ? ? ? ? ? ? Best,
> > ? ? ? ? ? ? ? ? ? ? ? ? Srishti
> > ? ? ? ? ? ? ? ? ? ? ? ? Social/Clinical Research Specialist
> > ? ? ? ? ? ? ? ? ? ? ? ? Child Imaging Research and Life
> Experiences Lab
> > ? ? ? ? ? ? ? ? ? ? ? ? University of North Carolina at
> Chapel 

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

can you email us the input file and the full command line you ran?
On Thu, 5 
Apr 2018, srishti goel wrote:



So it gave this error:

3d normalization pass 1 of 2

white matter peak found at 110

HISTOalloc(-2147483648): could not allocate histogram

Cannot allocate memory


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl  
wrote:
  let's see if it works. If it does, you should be able to run

  recon-all -s SUBJID -make all

  cheers
  Bruce


  On Thu, 5 Apr 2018, srishti goel wrote:

Should I re-run the recon-all after running the last command from 
recon-all.cmd?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl 
 wrote:
      Hi Srishti

      if you look in the subject's scripts dir there should be a file named 
"recon-all.cmd". Try
rerunning the last
      command in it (probably from the mri dir)

      cheers
      Bruce
      On Thu, 5 Apr 2018, srishti goel wrote:

            I am sorry, I am not sure what do you mean by running 
the command line directly?
            I use the following command:

            sbatch --mem 2200 -t 6-00:00 --mail-type END 
--mail-user srish...@email.unc.edu --wrap
"export
            
SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; 
recon-all -s 13166
            -autorecon2-cp -autorecon3 -nowmsa"


            where sbatch. until export is our local server 
submission command and I run this
command from the
            command line itself, not
            using any script.


            Best,
            Srishti
            Social/Clinical Research Specialist
            Child Imaging Research and Life Experiences Lab
            University of North Carolina at Chapel Hill
            email (W): srish...@email.unc.edu
            skype: srishti.goel12


            On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl 
 wrote:
                  if you run the command that failed again on the 
command line directly (that is, not
in
            recon-all) does it fail
                  again?

                  On Thu, 5 Apr 2018, srishti goel wrote:

                        Hi Bruce,

                        The machine definitely hasn't run out of 
memory. Here is the memory usage
                        from recon-all.log  

                                             total              
used        free                  
                        shared  buff/cache   available
                        Mem:      263726968    34330048   152102696 
      12944    77294224  
                        191963372
                        Swap:       2097148           0             
2097148




                        Best,
                        Srishti
                        Social/Clinical Research Specialist
                        Child Imaging Research and Life Experiences 
Lab
                        University of North Carolina at Chapel Hill
                        email (W): srish...@email.unc.edu
                        skype: srishti.goel12


                        On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl 

                        wrote:
                              Hi Srishti

                              are you sure that your machine didn't 
just run out of memory?
                              The recon-all.log file includes the 
amount of free (and total)
                              memory at the time the process was 
started.

                              cheers
                              Bruce

                               On Thu, 5 Apr 2018, srishti goel 
wrote:

                                    Hi,
                                    I have been trying to edit 
structural brains and
                                  

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[srishti goel]

So it gave this error:

3d normalization pass 1 of 2

white matter peak found at 110

HISTOalloc(-2147483648): could not allocate histogram

Cannot allocate memory

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl 
wrote:

> let's see if it works. If it does, you should be able to run
>
> recon-all -s SUBJID -make all
>
>
> cheers
> Bruce
>
>
> On Thu, 5 Apr 2018, srishti goel wrote:
>
> Should I re-run the recon-all after running the last command from
>> recon-all.cmd?
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl 
>> wrote:
>>   Hi Srishti
>>
>>   if you look in the subject's scripts dir there should be a file
>> named "recon-all.cmd". Try rerunning the last
>>   command in it (probably from the mri dir)
>>
>>   cheers
>>   Bruce
>>   On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> I am sorry, I am not sure what do you mean by running the
>> command line directly?
>> I use the following command:
>>
>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
>> srish...@email.unc.edu --wrap "export
>> 
>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>> recon-all -s 13166
>> -autorecon2-cp -autorecon3 -nowmsa"
>>
>>
>> where sbatch. until export is our local server submission
>> command and I run this command from the
>> command line itself, not
>> using any script.
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>>   if you run the command that failed again on the command
>> line directly (that is, not in
>> recon-all) does it fail
>>   again?
>>
>>   On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi Bruce,
>>
>> The machine definitely hasn't run out of memory.
>> Here is the memory usage
>> from recon-all.log
>>
>>  total  used
>>free
>> shared  buff/cache   available
>> Mem:  26372696834330048   152102696
>> 1294477294224
>> 191963372
>> Swap:   2097148   0
>> 2097148
>>
>>
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Srishti
>>
>>   are you sure that your machine didn't just
>> run out of memory?
>>   The recon-all.log file includes the amount
>> of free (and total)
>>   memory at the time the process was started.
>>
>>   cheers
>>   Bruce
>>
>>On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi,
>> I have been trying to edit structural
>> brains and
>> very few times I would get the
>> following error while
>> running recon-all -s
>> subjID
>>
>> white matter peak found at 110
>> cannot allocate memory
>>
>> Upon looking at the archive, there
>> was only one
>> similar issue and it was recommend to
>> check mri_info
>> as the brain mask might
>> have been corrupted. I did that and
>> here is the
>> output:

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

let's see if it works. If it does, you should be able to run

recon-all -s SUBJID -make all

cheers
Bruce


On Thu, 5 Apr 2018, srishti goel wrote:


Should I re-run the recon-all after running the last command from recon-all.cmd?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl  
wrote:
  Hi Srishti

  if you look in the subject's scripts dir there should be a file named 
"recon-all.cmd". Try rerunning the last
  command in it (probably from the mri dir)

  cheers
  Bruce
  On Thu, 5 Apr 2018, srishti goel wrote:

I am sorry, I am not sure what do you mean by running the command 
line directly?
I use the following command:

sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user 
srish...@email.unc.edu --wrap "export

SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; 
recon-all -s 13166
-autorecon2-cp -autorecon3 -nowmsa"


where sbatch. until export is our local server submission 
command and I run this command from the
command line itself, not
using any script.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl 
 wrote:
      if you run the command that failed again on the command line 
directly (that is, not in
recon-all) does it fail
      again?

      On Thu, 5 Apr 2018, srishti goel wrote:

            Hi Bruce,

            The machine definitely hasn't run out of memory. Here 
is the memory usage
            from recon-all.log  

                                 total              used        
free                  
            shared  buff/cache   available
            Mem:      263726968    34330048   152102696       12944 
   77294224  
            191963372
            Swap:       2097148           0             2097148




            Best,
            Srishti
            Social/Clinical Research Specialist
            Child Imaging Research and Life Experiences Lab
            University of North Carolina at Chapel Hill
            email (W): srish...@email.unc.edu
            skype: srishti.goel12


            On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl 

            wrote:
                  Hi Srishti

                  are you sure that your machine didn't just run 
out of memory?
                  The recon-all.log file includes the amount of 
free (and total)
                  memory at the time the process was started.

                  cheers
                  Bruce

                   On Thu, 5 Apr 2018, srishti goel wrote:

                        Hi,
                        I have been trying to edit structural 
brains and
                        very few times I would get the following 
error while
                        running recon-all -s
                        subjID

                        white matter peak found at 110
                        cannot allocate memory

                        Upon looking at the archive, there was only 
one
                        similar issue and it was recommend to check 
mri_info
                        as the brain mask might
                        have been corrupted. I did that and here is 
the
                        output:

                        Volume information for brainmask.mgz

                                  type: MGH

                            dimensions: 256 x 256 x 256

                           voxel sizes: 1.00, 1.00, 1.00

                                  type: UCHAR (0)

                                   fov: 256.000

                                   dof: 0

                                xstart: -128.0, xend: 128.0

                                ystart: -128.0, yend: 128.0

                                zstart: -128.0, zend: 128.0

                                    TR: 0.00 

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[srishti goel]

Should I re-run the recon-all after running the last command from
recon-all.cmd?

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl 
wrote:

> Hi Srishti
>
> if you look in the subject's scripts dir there should be a file named
> "recon-all.cmd". Try rerunning the last command in it (probably from the
> mri dir)
>
>
> cheers
> Bruce
> On Thu, 5 Apr 2018, srishti goel wrote:
>
> I am sorry, I am not sure what do you mean by running the command line
>> directly?
>> I use the following command:
>>
>> sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
>> srish...@email.unc.edu --wrap "export
>> SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
>> recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa"
>>
>>
>> where sbatch. until export is our local server submission command and
>> I run this command from the command line itself, not
>> using any script.
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl 
>> wrote:
>>   if you run the command that failed again on the command line
>> directly (that is, not in recon-all) does it fail
>>   again?
>>
>>   On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi Bruce,
>>
>> The machine definitely hasn't run out of memory. Here is the
>> memory usage
>> from recon-all.log
>>
>>  total  usedfree
>>
>> shared  buff/cache   available
>> Mem:  26372696834330048   152102696   12944
>>  77294224
>> 191963372
>> Swap:   2097148   0 2097148
>>
>>
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Srishti
>>
>>   are you sure that your machine didn't just run out of
>> memory?
>>   The recon-all.log file includes the amount of free (and
>> total)
>>   memory at the time the process was started.
>>
>>   cheers
>>   Bruce
>>
>>On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi,
>> I have been trying to edit structural brains and
>> very few times I would get the following error
>> while
>> running recon-all -s
>> subjID
>>
>> white matter peak found at 110
>> cannot allocate memory
>>
>> Upon looking at the archive, there was only one
>> similar issue and it was recommend to check
>> mri_info
>> as the brain mask might
>> have been corrupted. I did that and here is the
>> output:
>>
>> Volume information for brainmask.mgz
>>
>>   type: MGH
>>
>> dimensions: 256 x 256 x 256
>>
>>voxel sizes: 1.00, 1.00, 1.00
>>
>>   type: UCHAR (0)
>>
>>fov: 256.000
>>
>>dof: 0
>>
>> xstart: -128.0, xend: 128.0
>>
>> ystart: -128.0, yend: 128.0
>>
>> zstart: -128.0, zend: 128.0
>>
>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00
>> msec, flip angle: 0.00 degrees
>>
>>nframes: 1
>>
>>PhEncDir: UNKNOWN
>>
>>FieldStrength: 0.00
>>
>> ras xform present
>>
>> xform info: x_r =  -1., y_r =   0.,
>> z_r
>> =   0., c_r =-1.
>>
>>   : x_a =   0., y_a =   0.,
>> z_a
>> =   1., c_a =37.5000
>>
>>   : x_s =   0., y_s =  -1.,
>> z_s
>> =   0., c_s =  

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

Hi Srishti

if you look in the subject's scripts dir there should be a file named 
"recon-all.cmd". Try rerunning the last command in it (probably from the 
mri dir)


cheers
Bruce
On Thu, 5 Apr 2018, srishti goel wrote:


I am sorry, I am not sure what do you mean by running the command line directly?
I use the following command:

sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user srish...@email.unc.edu 
--wrap "export
SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/; recon-all -s 
13166 -autorecon2-cp -autorecon3 -nowmsa"


where sbatch. until export is our local server submission command and I run 
this command from the command line itself, not
using any script.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl  
wrote:
  if you run the command that failed again on the command line directly 
(that is, not in recon-all) does it fail
  again?

  On Thu, 5 Apr 2018, srishti goel wrote:

Hi Bruce,

The machine definitely hasn't run out of memory. Here is the memory 
usage
from recon-all.log  

                     total              used        free            
      
shared  buff/cache   available
Mem:      263726968    34330048   152102696       12944    77294224 
 
191963372
Swap:       2097148           0             2097148




Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl 

wrote:
      Hi Srishti

      are you sure that your machine didn't just run out of memory?
      The recon-all.log file includes the amount of free (and total)
      memory at the time the process was started.

      cheers
      Bruce

       On Thu, 5 Apr 2018, srishti goel wrote:

            Hi,
            I have been trying to edit structural brains and
            very few times I would get the following error while
            running recon-all -s
            subjID

            white matter peak found at 110
            cannot allocate memory

            Upon looking at the archive, there was only one
            similar issue and it was recommend to check mri_info
            as the brain mask might
            have been corrupted. I did that and here is the
            output:

            Volume information for brainmask.mgz

                      type: MGH

                dimensions: 256 x 256 x 256

               voxel sizes: 1.00, 1.00, 1.00

                      type: UCHAR (0)

                       fov: 256.000

                       dof: 0

                    xstart: -128.0, xend: 128.0

                    ystart: -128.0, yend: 128.0

                    zstart: -128.0, zend: 128.0

                        TR: 0.00 msec, TE: 0.00 msec, TI: 0.00
            msec, flip angle: 0.00 degrees

                   nframes: 1

                   PhEncDir: UNKNOWN

                   FieldStrength: 0.00

            ras xform present

                xform info: x_r =  -1., y_r =   0., z_r
            =   0., c_r =    -1.

                          : x_a =   0., y_a =   0., z_a
            =   1., c_a =    37.5000

                          : x_s =   0., y_s =  -1., z_s
            =   0., c_s =     4.7185


            talairach xfm 
:/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/talair
            ach.xfm

            Orientation   : LIA

            Primary Slice Direction: coronal


            voxel to ras transform:

                           -1.   0.   0.   127.

                            0.   0.   1.   -90.5000

                            0.  -1.   0.   132.7185

                            0.   0.   0.     1.


            voxel-to-ras determinant -1


            

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[srishti goel]

I am sorry, I am not sure what do you mean by running the command line
directly?

I use the following command:

sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
srish...@email.unc.edu --wrap "export
SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
recon-all -s 13166 -autorecon2-cp -autorecon3 -nowmsa"


where sbatch. until export is our local server submission command and I
run this command from the command line itself, not using any script.

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl 
wrote:

> if you run the command that failed again on the command line directly
> (that is, not in recon-all) does it fail again?
>
>
> On Thu, 5 Apr 2018, srishti goel wrote:
>
> Hi Bruce,
>>
>> The machine definitely hasn't run out of memory. Here is the memory usage
>> from recon-all.log
>>
>>  total  usedfree
>> shared  buff/cache   available
>> Mem:  26372696834330048   152102696   1294477294224
>> 191963372
>> Swap:   2097148   0 2097148
>>
>>
>>
>>
>> Best,
>> Srishti
>> Social/Clinical Research Specialist
>> Child Imaging Research and Life Experiences Lab
>> University of North Carolina at Chapel Hill
>> email (W): srish...@email.unc.edu
>> skype: srishti.goel12
>>
>>
>> On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl > >
>> wrote:
>>   Hi Srishti
>>
>>   are you sure that your machine didn't just run out of memory?
>>   The recon-all.log file includes the amount of free (and total)
>>   memory at the time the process was started.
>>
>>   cheers
>>   Bruce
>>
>>On Thu, 5 Apr 2018, srishti goel wrote:
>>
>> Hi,
>> I have been trying to edit structural brains and
>> very few times I would get the following error while
>> running recon-all -s
>> subjID
>>
>> white matter peak found at 110
>> cannot allocate memory
>>
>> Upon looking at the archive, there was only one
>> similar issue and it was recommend to check mri_info
>> as the brain mask might
>> have been corrupted. I did that and here is the
>> output:
>>
>> Volume information for brainmask.mgz
>>
>>   type: MGH
>>
>> dimensions: 256 x 256 x 256
>>
>>voxel sizes: 1.00, 1.00, 1.00
>>
>>   type: UCHAR (0)
>>
>>fov: 256.000
>>
>>dof: 0
>>
>> xstart: -128.0, xend: 128.0
>>
>> ystart: -128.0, yend: 128.0
>>
>> zstart: -128.0, zend: 128.0
>>
>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00
>> msec, flip angle: 0.00 degrees
>>
>>nframes: 1
>>
>>PhEncDir: UNKNOWN
>>
>>FieldStrength: 0.00
>>
>> ras xform present
>>
>> xform info: x_r =  -1., y_r =   0., z_r
>> =   0., c_r =-1.
>>
>>   : x_a =   0., y_a =   0., z_a
>> =   1., c_a =37.5000
>>
>>   : x_s =   0., y_s =  -1., z_s
>> =   0., c_s = 4.7185
>>
>>
>> talairach xfm :/pine/scr/s/r/srishtig/Duke_T
>> est/Freesurfer_out/11039/mri/transforms/talair
>> ach.xfm
>>
>> Orientation   : LIA
>>
>> Primary Slice Direction: coronal
>>
>>
>> voxel to ras transform:
>>
>>-1.   0.   0.   127.
>>
>> 0.   0.   1.   -90.5000
>>
>> 0.  -1.   0.   132.7185
>>
>> 0.   0.   0. 1.
>>
>>
>> voxel-to-ras determinant -1
>>
>>
>> ras to voxel transform:
>>
>>-1.  -0.  -0.   127.
>>
>>-0.  -0.  -1.   132.7185
>>
>>-0.   1.  -0.90.5000
>>
>>-0.  -0.  -0. 1.
>>
>>
>> Is there any other way to resolve this issue than
>> reconstruction the brain again and doing all the
>> edits all over again hoping
>> that the brain mask does not get corrupted this
>> time?
>>
>> Appreciate any help with this.
>>
>> Best,
>> Srishti
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

if you run the command that failed again on the command line directly (that 
is, not in recon-all) does it fail again?


On Thu, 5 Apr 2018, srishti goel wrote:


Hi Bruce,

The machine definitely hasn't run out of memory. Here is the memory usage
from recon-all.log  

                     total              used        free                  
shared  buff/cache   available
Mem:      263726968    34330048   152102696       12944    77294224  
191963372
Swap:       2097148           0             2097148




Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl 
wrote:
  Hi Srishti

  are you sure that your machine didn't just run out of memory?
  The recon-all.log file includes the amount of free (and total)
  memory at the time the process was started.

  cheers
  Bruce

   On Thu, 5 Apr 2018, srishti goel wrote:

Hi,
I have been trying to edit structural brains and
very few times I would get the following error while
running recon-all -s
subjID

white matter peak found at 110
cannot allocate memory

Upon looking at the archive, there was only one
similar issue and it was recommend to check mri_info
as the brain mask might
have been corrupted. I did that and here is the
output:

Volume information for brainmask.mgz

          type: MGH

    dimensions: 256 x 256 x 256

   voxel sizes: 1.00, 1.00, 1.00

          type: UCHAR (0)

           fov: 256.000

           dof: 0

        xstart: -128.0, xend: 128.0

        ystart: -128.0, yend: 128.0

        zstart: -128.0, zend: 128.0

            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00
msec, flip angle: 0.00 degrees

       nframes: 1

       PhEncDir: UNKNOWN

       FieldStrength: 0.00

ras xform present

    xform info: x_r =  -1., y_r =   0., z_r
=   0., c_r =    -1.

              : x_a =   0., y_a =   0., z_a
=   1., c_a =    37.5000

              : x_s =   0., y_s =  -1., z_s
=   0., c_s =     4.7185


talairach xfm 
:/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/talair
ach.xfm

Orientation   : LIA

Primary Slice Direction: coronal


voxel to ras transform:

               -1.   0.   0.   127.

                0.   0.   1.   -90.5000

                0.  -1.   0.   132.7185

                0.   0.   0.     1.


voxel-to-ras determinant -1


ras to voxel transform:

               -1.  -0.  -0.   127.

               -0.  -0.  -1.   132.7185

               -0.   1.  -0.    90.5000

               -0.  -0.  -0.     1.


Is there any other way to resolve this issue than
reconstruction the brain again and doing all the
edits all over again hoping
that the brain mask does not get corrupted this
time?

Appreciate any help with this.

Best,
Srishti


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The information in this e-mail is intended only for the person to whom
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[srishti goel]

Hi Bruce,

The machine definitely hasn't run out of memory. Here is the memory usage
from recon-all.log

 total  usedfree
shared  buff/cache   available
Mem:  26372696834330048   152102696   1294477294224
191963372
Swap:   2097148   0 2097148




Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl 
wrote:

> Hi Srishti
>
> are you sure that your machine didn't just run out of memory? The
> recon-all.log file includes the amount of free (and total) memory at the
> time the process was started.
>
> cheers
> Bruce
>
>
>  On Thu, 5 Apr 2018, srishti goel wrote:
>
> Hi,
>> I have been trying to edit structural brains and very few times I would
>> get the following error while running recon-all -s
>> subjID
>>
>> white matter peak found at 110
>> cannot allocate memory
>>
>> Upon looking at the archive, there was only one similar issue and it was
>> recommend to check mri_info as the brain mask might
>> have been corrupted. I did that and here is the output:
>>
>> Volume information for brainmask.mgz
>>
>>   type: MGH
>>
>> dimensions: 256 x 256 x 256
>>
>>voxel sizes: 1.00, 1.00, 1.00
>>
>>   type: UCHAR (0)
>>
>>fov: 256.000
>>
>>dof: 0
>>
>> xstart: -128.0, xend: 128.0
>>
>> ystart: -128.0, yend: 128.0
>>
>> zstart: -128.0, zend: 128.0
>>
>> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
>> degrees
>>
>>nframes: 1
>>
>>PhEncDir: UNKNOWN
>>
>>FieldStrength: 0.00
>>
>> ras xform present
>>
>> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
>> -1.
>>
>>   : x_a =   0., y_a =   0., z_a =   1., c_a =
>> 37.5000
>>
>>   : x_s =   0., y_s =  -1., z_s =   0., c_s =
>> 4.7185
>>
>>
>> talairach xfm : /pine/scr/s/r/srishtig/Duke_Te
>> st/Freesurfer_out/11039/mri/transforms/talairach.xfm
>>
>> Orientation   : LIA
>>
>> Primary Slice Direction: coronal
>>
>>
>> voxel to ras transform:
>>
>>-1.   0.   0.   127.
>>
>> 0.   0.   1.   -90.5000
>>
>> 0.  -1.   0.   132.7185
>>
>> 0.   0.   0. 1.
>>
>>
>> voxel-to-ras determinant -1
>>
>>
>> ras to voxel transform:
>>
>>-1.  -0.  -0.   127.
>>
>>-0.  -0.  -1.   132.7185
>>
>>-0.   1.  -0.90.5000
>>
>>-0.  -0.  -0. 1.
>>
>>
>> Is there any other way to resolve this issue than reconstruction the
>> brain again and doing all the edits all over again hoping
>> that the brain mask does not get corrupted this time?
>>
>> Appreciate any help with this.
>>
>> Best,
>> Srishti
>>
>>
> ___
> 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.
>
>
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Bruce Fischl]

Hi Srishti

are you sure that your machine didn't just run out of memory? The 
recon-all.log file includes the amount of free (and total) memory at the 
time the process was started.


cheers
Bruce

 On Thu, 5 Apr 
2018, srishti goel wrote:



Hi,
I have been trying to edit structural brains and very few times I would get the 
following error while running recon-all -s
subjID

white matter peak found at 110
cannot allocate memory

Upon looking at the archive, there was only one similar issue and it was 
recommend to check mri_info as the brain mask might
have been corrupted. I did that and here is the output:

Volume information for brainmask.mgz

          type: MGH

    dimensions: 256 x 256 x 256

   voxel sizes: 1.00, 1.00, 1.00

          type: UCHAR (0)

           fov: 256.000

           dof: 0

        xstart: -128.0, xend: 128.0

        ystart: -128.0, yend: 128.0

        zstart: -128.0, zend: 128.0

            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees

       nframes: 1

       PhEncDir: UNKNOWN

       FieldStrength: 0.00

ras xform present

    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    -1.

              : x_a =   0., y_a =   0., z_a =   1., c_a =    37.5000

              : x_s =   0., y_s =  -1., z_s =   0., c_s =     4.7185


talairach xfm : 
/pine/scr/s/r/srishtig/Duke_Test/Freesurfer_out/11039/mri/transforms/talairach.xfm

Orientation   : LIA

Primary Slice Direction: coronal


voxel to ras transform:

               -1.   0.   0.   127.

                0.   0.   1.   -90.5000

                0.  -1.   0.   132.7185

                0.   0.   0.     1.


voxel-to-ras determinant -1


ras to voxel transform:

               -1.  -0.  -0.   127.

               -0.  -0.  -1.   132.7185

               -0.   1.  -0.    90.5000

               -0.  -0.  -0.     1.


Is there any other way to resolve this issue than reconstruction the brain 
again and doing all the edits all over again hoping
that the brain mask does not get corrupted this time?

Appreciate any help with this.

Best,
Srishti

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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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