Re: [Freesurfer] Recon-all exited without errors

[Douglas N. Greve]

That one looks like there was a massive failure of the registration. One 
thing you can try is to add -samseg-reg to the command line. This will 
use samseg to do this registration, which may be more robust. Is there 
anything amiss with your image?


On 2/13/2023 10:25 AM, Goeckner, Bryna wrote:


External Email - Use Caution

Thanks for the response.  I should have been more clear in my first 
email.  I have used tkregister2 in the past to fix talairachs, but 
this one does not appear to be fixable with the in-plane shifting, 
scaling, and rotating that is available within the tkregister2 GUI.  
The moveable appears to be in a different plane than the target. I’m 
attaching a screenshot from tkregister2.


Is there a different way to fix the talairach or another recon fix 
(especially considering the apparent brainmask issue) that should be 
pursued?


Thanks again for your help!

*Bryna Goeckner* (she/her)

Graduate Student

Meier Lab

Medical College of Wisconsin

Neuroscience Doctoral Program

Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing" 
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list 
Message-ID:


Content-Type: text/plain; charset="us-ascii"

Hi Bryna,

In this tutorial, it talks about how to fix bad output from the 
talairach registration:


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://urldefense.com/v3/__https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$ 
<https://secure-web.cisco.com/1HZhWFe_X3bRyu1YMrXe-GHFqQMAp04dAp8aVbI-P4-kd9XuX7fVsWdo1N2FV-BK7Kbf14_mEbYcXBej0M7TxUI7FxJQn3tng1J51U4hRi6nWKqOVDjTQW9jAl1K5WpUp9DHONveLfGOggQk-eQOGTf6wFZcvs9mW9PKB5ewCbuL7PDrj1TZ_8uLc1Tok2eS4q24SZBfZcAiNNTjfLW1EdnIaPouA3ruo1ZSk0hOUYTMzcKamBpdVrUjcMHmI6SQEMhGj7_9lxwuB28WuR_Q_IFQLF6vFx7W_lnh8vtBlI0akxRMt_YFuxDJVCWcJvxPW4ohMXUYGOWgJznRPRJrH7w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__%3B%21%21H8mHWRdzp34%21_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY%24>


Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Goeckner, Bryna

Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors


    External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with 
errors (looks like for talairach issues) but I am not able to use 
tkregister2 to view and make manual adjustments to the talairach since 
surf/lh.orig was not generated.


I then tried recon-all with the -notal-check flag, which exited 
"without errors" although the talairach is nowhere near correctly 
aligned and while aparc & aseg in freeview appear ok, the brainmask 
appears to have issues (when I turn it off, the entire background 
displays as white).


I'm including the recon-all logs (original & notal-check flag) and 
have listed the actual commands used below as well.  Any help you can 
provide in figuring out how to run this subject is greatly 
appreciated.  Thanks!


The original code was:
recon-all -subject subj# \
    -i rawT1.nii.gz \
    -T2 rawT2.nii.gz \
    -T2pial \
    -parallel -openmp 12 \
    -3T \
    -all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program


___
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Re: [Freesurfer] Recon-all exited without errors

[Goeckner, Bryna]

External Email - Use Caution

Thanks for the response.  I should have been more clear in my first email.  I 
have used tkregister2 in the past to fix talairachs, but this one does not 
appear to be fixable with the in-plane shifting, scaling, and rotating that is 
available within the tkregister2 GUI.  The moveable appears to be in a 
different plane than the target. I’m attaching a screenshot from tkregister2.

Is there a different way to fix the talairach or another recon fix (especially 
considering the apparent brainmask issue) that should be pursued?

Thanks again for your help!

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program

Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing" 
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list 
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Hi Bryna,

In this tutorial, it talks about how to fix bad output from the talairach 
registration:

https://secure-web.cisco.com/1AsdowaGUQbpsRB4dUWGRiDD2RdKWB-n1kUwwmPwq1WQ9YeKKqov5FFLfo7EJ1tkbdCb8krY7nQttKhgmNZCXK5L94ZpFhJkWTFUHHIAx2IOPV6NdbjrrR8l5to2eYyjf7f73q0gxzvGRqPjFYJSbx6RnU2e6Y0Y845X5iZK0gJjKf0ocZfzbtnDxSQPa9rAacjR4rEiApsikJTcm8bqKneABuY85pIGXSVGaAlmOYhwc2jnJOim5ip-CHBIWC6YBOUNw73onOe9612EeLkDlFEN7mTxvA6ddcLM4B5FXXvr0imuo4Q0yko_o4jFQXiRG_YNEBEk4HApUCE4KmVHr2w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$<https://secure-web.cisco.com/1YTUJIwB-u_KNhoI17IHgKhkMu-K4cxIGnnOeSiooClREnWme11f5wwS_mX9Rx4UP523Br2Cnzb57bqvcJ2PLBpiR5k410ksn7Q23xaG_tnK045KUyPlp2rv7s6Kq2pte4t73E-NqHvoLJFuWAySX2iOqlRGRmOaLPmHkm5Vk9y5Jj5SO3Ndt8nUQS657skk6jrPN5DJXr8S4FayfpfrGAxz9djtI9_5v63yyeGK9B7IHShMLkrd7mOgTgg91nQQ8j57F_1qykXxnrxZ1SEHy714L5pyC2GzySNFbxWd0_mqGSYYIxDNNLByDVDIEeNVktgup-0CUh10JQIsW5HhPUQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$>

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Goeckner, Bryna
Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors


External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with errors 
(looks like for talairach issues) but I am not able to use tkregister2 to view 
and make manual adjustments to the talairach since surf/lh.orig was not 
generated.

I then tried recon-all with the -notal-check flag, which exited "without 
errors" although the talairach is nowhere near correctly aligned and while 
aparc & aseg in freeview appear ok, the brainmask appears to have issues (when 
I turn it off, the entire background displays as white).

I'm including the recon-all logs (original & notal-check flag) and have listed 
the actual commands used below as well.  Any help you can provide in figuring 
out how to run this subject is greatly appreciated.  Thanks!

The original code was:
recon-all -subject subj# \
-i rawT1.nii.gz \
-T2 rawT2.nii.gz \
-T2pial \
-parallel -openmp 12 \
-3T \
-all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
___
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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 Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Recon-all exited with errors

[Huang, Yujing]

Hi Bryna,

In this tutorial, it talks about how to fix bad output from the talairach 
registration:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Goeckner, Bryna
Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors


External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with errors 
(looks like for talairach issues) but I am not able to use tkregister2 to view 
and make manual adjustments to the talairach since surf/lh.orig was not 
generated.

I then tried recon-all with the -notal-check flag, which exited "without 
errors" although the talairach is nowhere near correctly aligned and while 
aparc & aseg in freeview appear ok, the brainmask appears to have issues (when 
I turn it off, the entire background displays as white).

I'm including the recon-all logs (original & notal-check flag) and have listed 
the actual commands used below as well.  Any help you can provide in figuring 
out how to run this subject is greatly appreciated.  Thanks!

The original code was:
recon-all -subject subj# \
-i rawT1.nii.gz \
-T2 rawT2.nii.gz \
-T2pial \
-parallel -openmp 12 \
-3T \
-all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier 
Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
___
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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Re: [Freesurfer] recon-all exited with ERRORS

[Douglas N. Greve]

Not sure what you are trying to do. Usually we do not do voxel-wise 
analysis on the asegs (eg, like with a vbm)


On 8/29/2021 2:52 PM, guang wrote:


External Email - Use Caution







At 2021-08-05 08:44:11, "guang"  wrote:

Hello FreeSurfer Developers,
I'm trying to analyze aseg.mgz files for each subjects though i
have segmented  hippocampal subfields and nuclei of the amygdala.
Can I make the voxel-by voxel group analysis with the aseg.mgz or
the  aparc+aseg.mgz files?

Thank you  for any reply.

guang






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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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all exited with ERRORS

[guang]

External Email - Use Caution


















At 2021-08-05 08:44:11, "guang"  wrote:

Hello FreeSurfer Developers,
I'm trying to analyze aseg.mgz files for each subjects though i have segmented  
hippocampal subfields and nuclei of the amygdala. Can I make the voxel-by voxel 
group analysis with the aseg.mgz or the  aparc+aseg.mgz files?


Thank you  for any reply.


guang






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Re: [Freesurfer] recon-all exited with ERRORS

[fsbuild]

External Email - Use Caution

If you are running Virtualbox to host linux on a windows machine sharing a 
folder from a windows NTFS file system, then it may not work to create soft 
links in linux on the mounted share w/o setting some things on the Windows 
side. I’m not up on what current versions of VirtualBox support for 
creating soft links in a linux file system on top of the (different) NTFS file 
system, but here is some info from ~2 years 
ago,https://secure-web.cisco.com/1FAdsc9WBYl3JetwHMp2nc_AR2rQlI8PlEU1VIVMmtW4AXXraRYQrh4EesIh-2zxLL95RZ4uADb94HhLf6bwC4HStrmNBxTN1P6onMGfuO2S4W4uvvwfGIBNqjQiVAZPmx6apNd4RkD__6429s9Dec_A80QMbmZ5p1jH5eSbN_Yy8sjxqJeDxkuw6X14AqP-wtxc7-bvAz65_QiVsYkX5NYR7HCd7X9LJ_qmhN6nk5ccXH_x6XDx5euZhGR99v6Dj/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F56343002%2Fis-it-possible-to-use-symbolic-links-in-virtualbox-shared-folder-without-adminis
- R.

On Aug 5, 2021, at 10:20, Kiyotaka Nemoto kiyot...@nemotos.net 
wrote:External Email - Use 
CautionHi,I think the problem 
is caused because Zhaoguanguses a VirtualBox share folder.The path 
"/media/sf_T1/" indicates the path is a shared folder of VirtualBox.Symbolic 
links can be used on some certain conditions.Source:MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1SzkQ16diCzjzLRbWT9fZxbUN_qVihhNUAbkqhDWMHpIn3-M2UeXKZtomyLdGKz2hQxzBRgbN5ye_n05Zfy6i5YNSm-x-25yEjp6h819_yq-6XkkGYt7FEZuwuuolHCQWTR-sqNub0Pf4T8SZ5ech1a-XOt0R2j7pKbYcP2AiDn1AZEeiN-1FzCbzAd1OPrZdpQWmDKTLuEUcQI_l28duTwPlf-3v0aiOLOQGoQ_n2r2o86c1tP5E7kGLa3LF4bPG/https%3A%2F%2Fwww.virtualbox.org%2Fmanual%2FUserManual.html%23sharedfoldersI
 think there are two workaround options..1. Avoid using shared folders 
 If you copy your T1 image from shared folder to somewhere on your Linux 
guest, recon-all should go well.2. Change "ln -s" to "cp" in recon-all 
 I tweak recon-all a little bit so that recon-all works well with files 
on VirtualBox shared folders.  The commands below makes backup of 
recon-all first, then substitute "ln -s" with "cp" or "cp -r"=cd 
$FREESURFER_HOME/binsudo cp recon-all recon-all.origsudo sed -i 's/ln -s 
\$hemi/cp \$hemi/' recon-allsudo sed -i 's/ln -s 
\$FREESURFER_HOME\/subjects\/fsaverage/cp -r 
\$FREESURFER_HOME\/subjects\/fsaverage \$SUBJECTS_DIR/' recon-allsudo sed -i 
's/ln -s \$FREESURFER_HOME\/subjects\/\${hemi}.EC_average/cp -r 
\$FREESURFER_HOME\/subjects\/\${hemi}.EC_average \$SUBJECTS_DIR/' 
recon-all=Hope this helps,KiyotakaOn Thu, Aug 5, 2021 at 10:42 PM Douglas 
N. Greve dgr...@mgh.harvard.edu wrote:Look in 
/media/sf_T1/recon/demo3/surfDoes lh.white.preaparc.H exist?If so, does 
lh.white.H exist?If not, what happens when you runln -s lh.white.preaparc.H 
lh.white.Hin that folder?On 8/5/2021 1:41 AM, guang 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I'm attempting to preprocess my nii.gz files with FreeSurfer, But 
some errorsoccurred when I recon-all the data. I've attached 
the batch script and recon-all.log in case it's of any use.1) 
FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0..0-2beb96c2) Platform: CentOS 
release 6.10 (Final)3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP 
Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux4) recon-all.log: 
see attached5) batch .shfile:seeattachedThank you for any 
reply.zhaoguang___
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 mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1II6DOs_uxItsRQUh3upLmjq_rgOJnRtQnqFDe1XOdS2eNb64q9B53FQku5EjESybzvgxx0LXKF9uHBO5zwFvd1EebEKmeqdWrtwaUenm6DrpyrP3lFjys3dkRFQyYNt_O-6ZJa7PXeqEks9-dBOxA4lTJQUZ0QcUTHlkKMffDn0zQh6VPZupZcWm6s1k0Mz8rVr72izrYB11UUOZYtMfDN-YGyswQsrW9xSFTZhY_34xfo29hzuPD4ym8t_qNMZf/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe
 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 Mass General Brigham 
Compliance HelpLine atMailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to 

Re: [Freesurfer] recon-all exited with ERRORS

[Kiyotaka Nemoto]

External Email - Use Caution

Hi,

I think the problem is caused because Zhaoguang uses a VirtualBox share
folder.
The path "/media/sf_T1/" indicates the path is a shared folder of
VirtualBox.

Symbolic links can be used on some certain conditions.
Source: 
https://secure-web.cisco.com/1dwlgJDipuhkA56EdBKvdgjX7GQ06QB_tibWCFgxRVp5qMyNCdaPDbahbXesxHSWfDY3t8wvp6OTfje04KDpgHFGDdkoecJv07GtKeuldJJNVJnsuffSVx9LfYzLYeh-1a5ScJN1PdZ-fDNE--Lnv1R4phboTjurWMX43qna0wem5Wa2vhWvLXwEfcGTxqY7Bduq1xk_MKqmJ0BaQptL5lOK-V0kBUTl58fCB2eRrlvBQMoLDzBscjG_cnGqeT3ZMyhoh1X1rv5D7bkil9-4mWA/https%3A%2F%2Fwww.virtualbox.org%2Fmanual%2FUserManual.html%23sharedfolders

I think there are two workaround options.

1. Avoid using shared folders
If you copy your T1 image from shared folder to somewhere on your Linux
guest, recon-all should go well.

2. Change "ln -s" to "cp" in recon-all
I tweak recon-all a little bit so that recon-all works well with files
on VirtualBox shared folders.
The commands below makes backup of recon-all first, then substitute "ln
-s" with "cp" or "cp -r"

=
cd $FREESURFER_HOME/bin
sudo cp recon-all recon-all.orig

sudo sed -i 's/ln -s \$hemi/cp \$hemi/' recon-all
sudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/fsaverage/cp -r
\$FREESURFER_HOME\/subjects\/fsaverage \$SUBJECTS_DIR/' recon-all
sudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/\${hemi}.EC_average/cp -r
\$FREESURFER_HOME\/subjects\/\${hemi}.EC_average \$SUBJECTS_DIR/' recon-all
=

Hope this helps,

Kiyotaka



On Thu, Aug 5, 2021 at 10:42 PM Douglas N. Greve 
wrote:

> Look in /media/sf_T1/recon/demo3/surf
> Does lh.white.preaparc.H exist?
> If so, does lh.white.H exist?
> If not, what happens when you run
> ln -s lh.white.preaparc.H lh.white.H
> in that folder?
>
>
>
> On 8/5/2021 1:41 AM, guang wrote:
>
> External Email - Use Caution
> Hello FreeSurfer Developers,
> I'm attempting to preprocess my nii.gz files with FreeSurfer, But some
> errors occurred  when I  recon-all the data. I've attached the batch script
> and  recon-all.log in case it's of any use.
> 1) FreeSurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 2) Platform: CentOS release 6.10 (Final)
> 3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13
> 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> 4) recon-all.log: see attached
> 5) batch .sh file:see attached
>
> Thank you  for any reply.
>
> zhaoguang
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing 
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Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
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Re: [Freesurfer] recon-all exited with ERRORS

[Douglas N. Greve]

Look in /media/sf_T1/recon/demo3/surf
Does lh.white.preaparc.H exist?
If so, does lh.white.H exist?
If not, what happens when you run
ln -s lh.white.preaparc.H lh.white.H
in that folder?



On 8/5/2021 1:41 AM, guang wrote:


External Email - Use Caution

Hello FreeSurfer Developers,
I'm attempting to preprocess my nii.gz files with FreeSurfer, But some 
errors occurred  when I recon-all the data. I've attached the batch 
script and recon-all.log in case it's of any use.
1) FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: CentOS release 6.10 (Final)
3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 
12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

4) recon-all.log: see attached
5) batch .sh file:see attached

Thank you  for any reply.

zhaoguang






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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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all exited with errors

[Vinny K]

External Email - Use Caution

Thanks Douglas.  I downloaded and installed the latest version 7.1.1 and
recon-all with no errors.

On Tue., Sep. 1, 2020, 10:21 a.m. Douglas Greve, 
wrote:

> Try looking at our wiki
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
>
>
> On 8/30/20 7:16 AM, Vinny K wrote:
>
> External Email - Use Caution
> Hi,
>
> I've tried to process a scan but it gets hung up on a particular large
> defect and then exits with error.  I've had large defects with other scans
> before but recon-all was able to get past it.  How can I correct this?
> I've attached the recon-all log.
>
> Thanks,
>
> Vinny
>
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Re: [Freesurfer] recon-all exited with errors

[Douglas Greve]

Try looking at our wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview


On 8/30/20 7:16 AM, Vinny K wrote:


External Email - Use Caution

Hi,

I've tried to process a scan but it gets hung up on a particular large 
defect and then exits with error.  I've had large defects with other 
scans before but recon-all was able to get past it.  How can I correct 
this?  I've attached the recon-all log.


Thanks,

Vinny

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Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

[Douglas N. Greve]

Does
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/label/lh.cortex.label
exist?

On 5/7/2020 11:33 AM, Mason Wells wrote:


External Email - Use Caution

Terminal output is below:

export 
SUBJECTS_DIR=/home/c1749990/Documents/Analysis/Data/freesurfer/subjects


c1749990@l029:~/Documents/Analysis/Data/PMA_retinoScans/PPT_004$ 
recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 
-label_v1


recon-all -i pre_processed_anatomy/T1.nii.gz -s PPT_004 -parcstats3 
-label_v1


Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects


Actual FREESURFER_HOME /cubric/software/freesurfer.versions/5.3.0

Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 
29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux


/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004

mri_convert 
/home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz 



mri_convert 
/home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz 



$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/home/c1749990/Documents/Analysis/Data/PMA_retinoScans/PPT_004/pre_processed_anatomy/T1.nii.gz...


TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 1, 0)

k_ras = (0, 0, 1)

writing to 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/mri/orig/001.mgz...


#-

#@# Parcellation Stats 3 lh Thu May  7 16:32:30 BST 2020

/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a 
../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_004 lh white


No such file or directory

mris_anatomical_stats: could not open label file ../label/lh.cortex.label

INFO: assuming MGZ format for volumes.

Invalid argument

Invalid argument

Linux l029.cubric.cf.ac.uk 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr 
29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s PPT_004 exited with ERRORS at Thu May  7 16:32:30 BST 2020

For more details, see the log file 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_004/scripts/recon-all.log


To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Thursday, 7 May 2020 at 15:59
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

No all, just one. And try running it with just the -parcstats3 flag 
(ie, don't use -all or -autreconX). You should have an answer in seconds


On 5/7/2020 7:50 AM, Mason Wells wrote:

*External Email - Use Caution *

Hi Doug,

Sorry I am a bit confused. I ran recon-all as a bash for 30
participants. None of which had the right hemisphere completed and
recon-all log says exited with errors (as the log in the original
email shows). Are you suggesting I go back and re-run recon-all
via the bash and see if I get the same issue?

Thanks for all your help.

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(C

Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

[Douglas N. Greve]

No all, just one. And try running it with just the -parcstats3 flag (ie, 
don't use -all or -autreconX). You should have an answer in seconds


On 5/7/2020 7:50 AM, Mason Wells wrote:


External Email - Use Caution

Hi Doug,

Sorry I am a bit confused. I ran recon-all as a bash for 30 
participants. None of which had the right hemisphere completed and 
recon-all log says exited with errors (as the log in the original 
email shows). Are you suggesting I go back and re-run recon-all via 
the bash and see if I get the same issue?


Thanks for all your help.

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Wednesday, 6 May 2020 at 23:11
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors

It looks like that command finished without error. Have you tried 
running it in recon-all again to see if it fails again? You can just 
run that command with -parcstats3


On 5/6/2020 6:41 AM, Mason Wells wrote:

*External Email - Use Caution *

Hi Doug,

Not sure if my email below got to you? I sent the terminal outputs
of the command you told me to run. Any idea what’s going on or how
to fix it?

Cheers,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: *
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mason
Wells  <mailto:wells...@cardiff.ac.uk>
*Reply to: *Freesurfer support list

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, 4 May 2020 at 20:01
*To: *Freesurfer support list 
    <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

*External Email - Use Caution *

Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.DKTatlas40.stats -b -a
../label/lh.aparc.DKTatlas40.annot -c
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white

INFO: assuming MGZ format for volumes.

INFO: using ../label/lh.cortex.label as mask to calc cortex
NumVert, SurfArea and MeanThickness.

computing statistics for each annotation in
../label/lh.aparc.DKTatlas40.annot.

reading volume

/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...

reading input surface

/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...

reading input pial surface

/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...

reading input white surface

/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...

reading colortable from annotation file...

colortable with 36 entries read (originally
/Applications/freesurfer/average/colortable_desikan_killiany.txt)

Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab

table columns are:

number of vertices

total surface area (mm^2)

total gray matter volume (mm^3)

average cortical thickness +- standard deviation (mm)

integrated rectified mean curvature

integrated rectified Gaussian curvature

folding index

intrinsic curvature index

structure name

1698 1132   3274  2.730 0.526 0.130 0.032   26 2.4 

Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

[Mason Wells]

External Email - Use Caution

Hi Doug,

Sorry I am a bit confused. I ran recon-all as a bash for 30 participants. None 
of which had the right hemisphere completed and recon-all log says exited with 
errors (as the log in the original email shows). Are you suggesting I go back 
and re-run recon-all via the bash and see if I get the same issue?

Thanks for all your help.
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Wednesday, 6 May 2020 at 23:11
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Recon-all exited WITH errors

It looks like that command finished without error. Have you tried running it in 
recon-all again to see if it fails again? You can just run that command with 
-parcstats3

On 5/6/2020 6:41 AM, Mason Wells wrote:

External Email - Use Caution
Hi Doug,

Not sure if my email below got to you? I sent the terminal outputs of the 
command you told me to run. Any idea what’s going on or how to fix it?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Mason Wells 
<mailto:wells...@cardiff.ac.uk>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 4 May 2020 at 20:01
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}


External Email - Use Caution
Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea 
and MeanThickness.
computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...
reading input surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
reading input pial surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...
reading input white surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
reading colortable from annotation file...
colortable with 36 entries read (originally 
/Applications/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

1698   1132   3274  2.730 0.526 0.130 0.032   26 2.4  
caudalanteriorcingulate
4375   2908   8369  2.594 0.599 0.127 0.040   46 7.0  
caudalmiddlefrontal
3883   2464   5378  2.087 0.498 0.149 0.082   74 9.4  cuneus
  546373   1423  2.817 0.999 0.154 0.087   11 1.9  
entorhinal
5411   3506  10979  2.768 0.567 0.137 0.059  10114.8  fusiform
6159   4159  11629  2.543 0.520 0.133 0.045   8611.0  
inferiorparietal
5973   3945  13736  2.965 0.705 0.138 0.060  13013.4  
inferiortemporal
1536934   2788  2.725 0.838 0.164 0.090   50 5.1  
isthmuscingulate
695

Re: [Freesurfer] Recon-all exited WITH errors

[Douglas N. Greve]

It looks like that command finished without error. Have you tried 
running it in recon-all again to see if it fails again? You can just run 
that command with -parcstats3



On 5/6/2020 6:41 AM, Mason Wells wrote:


External Email - Use Caution

Hi Doug,

Not sure if my email below got to you? I sent the terminal outputs of 
the command you told me to run. Any idea what’s going on or how to fix it?


Cheers,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of Mason 
Wells 

*Reply to: *Freesurfer support list 
*Date: *Monday, 4 May 2020 at 20:01
*To: *Freesurfer support list 
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

*External Email - Use Caution *

Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a 
../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white


INFO: assuming MGZ format for volumes.

INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, 
SurfArea and MeanThickness.


computing statistics for each annotation in 
../label/lh.aparc.DKTatlas40.annot.


reading volume 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...


reading input surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...


reading input pial surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...


reading input white surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...


reading colortable from annotation file...

colortable with 36 entries read (originally 
/Applications/freesurfer/average/colortable_desikan_killiany.txt)


Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab

table columns are:

number of vertices

total surface area (mm^2)

total gray matter volume (mm^3)

average cortical thickness +- standard deviation (mm)

integrated rectified mean curvature

integrated rectified Gaussian curvature

folding index

intrinsic curvature index

structure name

1698 1132   3274  2.730 0.526 0.130 0.032   26 2.4  
caudalanteriorcingulate


4375 2908   8369  2.594 0.599 0.127 0.040   46 7.0  
caudalmiddlefrontal


3883 2464   5378  2.087 0.498 0.149 0.082   74 9.4  cuneus

546    373   1423  2.817 0.999 0.154 0.087 11 1.9  entorhinal

5411 3506  10979  2.768 0.567 0.137 0.059  101 14.8  fusiform

6159 4159  11629  2.543 0.520 0.133 0.045   86 11.0  
inferiorparietal


5973 3945  13736  2.965 0.705 0.138 0.060  130 13.4  
inferiortemporal


1536 934   2788  2.725 0.838 0.164 0.090   50 5.1  
isthmuscingulate


6953 4476  11030  2.320 0.542 0.147 0.055  110 15.3  
lateraloccipital


3897 2512   7780  2.641 0.630 0.147 0.077   99 13.1  
lateralorbitofrontal


5273 3237   7567  2.161 0.603 0.151 0.956  191 20.8  lingual

2015 1290   4210  2.576 0.773 0.157 0.084   64 6.5  
medialorbitofrontal


6073 4091  14456  3.026 0.553 0.130 0.043   80 11.0  
middletemporal


1012 711   2254  2.886 0.735 0.133 0.112   16 6.3  
parahippocampal


2182 1401   4296  2.690 0.669 0.128 0.044   26 4.5  
paracentral


3247 2175   6722  2.682 0.501 0.121 0.038   34 5.1  
parsopercularis


1195 793   2520  2.549 0.514 0.138 0.045   21 2.1  
parsorbitalis


2780 1882   5377  2.457 0.608 0.131 0.043   37 5.0  
parstriangularis


2229 1444   2359  1.685 0.476 0.155 0.067   41 6.1  
pericalcarine


7692 4818  11728  2.218 0.657 0.130 0.053  114 16.0  
postcentral


1983 1360   4109  2.902 0.617 0.167 0.079   44 6.1  
posteriorcingulate


7681 4765  13220  2.521 0.549 0.123 0.056  119 15.1  
precentral


6240 4189  11573  2.532 0.576 0.145 0.052  104 13.3  precuneus

1613 992   3166  2.820 0.661 0.136 0.055   54 3.6  
rostralanteriorcingulate


6644 4495  12118  2.347 0.579 0.144 0.052  117 13.9  
rostralmiddlefrontal


12967 8768  28469  2.839 0.612 0.132 0.047  

Re: [Freesurfer] Recon-all exited WITH errors

[Mason Wells]

External Email - Use Caution

Hi Doug,

Not sure if my email below got to you? I sent the terminal outputs of the 
command you told me to run. Any idea what’s going on or how to fix it?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of Mason Wells 

Reply to: Freesurfer support list 
Date: Monday, 4 May 2020 at 20:01
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}


External Email - Use Caution
Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out below:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea 
and MeanThickness.
computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/mri/wm.mgz...
reading input surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
reading input pial surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.pial...
reading input white surface 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/surf/lh.white...
reading colortable from annotation file...
colortable with 36 entries read (originally 
/Applications/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

1698   1132   3274  2.730 0.526 0.130 0.032   26 2.4  
caudalanteriorcingulate
4375   2908   8369  2.594 0.599 0.127 0.040   46 7.0  
caudalmiddlefrontal
3883   2464   5378  2.087 0.498 0.149 0.082   74 9.4  cuneus
  546373   1423  2.817 0.999 0.154 0.087   11 1.9  
entorhinal
5411   3506  10979  2.768 0.567 0.137 0.059  10114.8  fusiform
6159   4159  11629  2.543 0.520 0.133 0.045   8611.0  
inferiorparietal
5973   3945  13736  2.965 0.705 0.138 0.060  13013.4  
inferiortemporal
1536934   2788  2.725 0.838 0.164 0.090   50 5.1  
isthmuscingulate
6953   4476  11030  2.320 0.542 0.147 0.055  11015.3  
lateraloccipital
3897   2512   7780  2.641 0.630 0.147 0.077   9913.1  
lateralorbitofrontal
5273   3237   7567  2.161 0.603 0.151 0.956  19120.8  lingual
2015   1290   4210  2.576 0.773 0.157 0.084   64 6.5  
medialorbitofrontal
6073   4091  14456  3.026 0.553 0.130 0.043   8011.0  
middletemporal
1012711   2254  2.886 0.735 0.133 0.112   16 6.3  
parahippocampal
2182   1401   4296  2.690 0.669 0.128 0.044   26 4.5  
paracentral
3247   2175   6722  2.682 0.501 0.121 0.038   34 5.1  
parsopercularis
1195793   2520  2.549 0.514 0.138 0.045   21 2.1  
parsorbitalis
2780   1882   5377  2.457 0.608 0.131 0.043   37 5.0  
parstriangularis
2229   1444   2359  1.685 0.476 0.155 0.067   41 6.1  
pericalcarine
7692   4818  11728  2.218 0.657 0.130 0.053  11416.0  
postcentral
1983   1360   4109  2.902 0.617 0.167 0.079   44 6.1  
posteriorcingulate
7681   4765  13220  2.521 0.549 0.123 0.056  11915.1  precentral
6240   4189  11573  2.532 0.576 0.145 0.052  10413.3  precuneus
1613992   3166  2.820 0.661 0.136 0.055   54 3.6  
rostralanteriorcingulate
6644   4495  12118  2.347 0.579 0.144 0.052  11713.9  
rostralmiddlefrontal
12967   8768  28469  2.839 0.612 0.132 0.047  17025.1  
superiorfrontal
7963   5213  12201  2.095 0.481 0.125 0.053  12516.2  
superiorparietal
9021   6069  20753  3.059 0.612 0.130 0.050  183 

Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

[Mason Wells]

;freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

Something else has gone wrong. wm.mgz should have been there in order to get as 
far as it did. Is your SUBJECTS_DIR set properly?
On 5/4/2020 2:49 PM, Mason Wells wrote:

External Email - Use Caution
Hi,

Terminal output is below:

/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ 
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea 
and MeanThickness.
computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...
mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): 
could not open file
mris_anatomical_stats: could not read input volume 
/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply to: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 4 May 2020 at 18:54
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exited WITH errors

Unfortunately, the log file does not indicate what went wrong. But it does show 
that the error happened on the LH (so it is not just RH). Run the command below 
and send all terminal output

cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white



On 5/4/2020 1:34 PM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

I appear to be having some issues with recon-all. I ran the command from a bash 
script (see attached), and it appears to work fine for the left hemisphere as 
the correct files are in the surf folder. However, there are no right 
hemisphere surf files. I have attached the log and error log for PPT01 and 
PPT02. Any advice on as to why this has happened would be great.

Thanks in advance,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628





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Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

[Douglas N. Greve]

Something else has gone wrong. wm.mgz should have been there in order to 
get as far as it did. Is your SUBJECTS_DIR set properly?


On 5/4/2020 2:49 PM, Mason Wells wrote:


External Email - Use Caution

Hi,

Terminal output is below:

/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ 
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a 
../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white


INFO: assuming MGZ format for volumes.

INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, 
SurfArea and MeanThickness.


computing statistics for each annotation in 
../label/lh.aparc.DKTatlas40.annot.


reading volume 
/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...


mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, 
-1): could not open file


mris_anatomical_stats: could not read input volume 
/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz


Cheers,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 
<https://www.cardiff.ac.uk/people/research-students/view/974214->




*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Monday, 4 May 2020 at 18:54
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors

Unfortunately, the log file does not indicate what went wrong. But it 
does show that the error happened on the LH (so it is not just RH). 
Run the command below and send all terminal output


cd 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a 
../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white



On 5/4/2020 1:34 PM, Mason Wells wrote:

*External Email - Use Caution *

Hi Experts,

I appear to be having some issues with recon-all. I ran the
command from a bash script (see attached), and it appears to work
fine for the left hemisphere as the correct files are in the surf
folder. However, there are no right hemisphere surf files. I have
attached the log and error log for PPT01 and PPT02. Any advice on
as to why this has happened would be great.

Thanks in advance,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk <mailto:wells...@cardiff.ac.uk>

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage
<https://www.cardiff.ac.uk/people/research-students/view/974214->



*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd
(CUBRIC), Yr Ysgol Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk <mailto:wells...@caerdydd.ac.uk>

*/Ffôn/*: 02920 879628



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Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}

[Mason Wells]

External Email - Use Caution

Hi,

Terminal output is below:

/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts$ 
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea 
and MeanThickness.
computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz...
mghRead(/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz, -1): 
could not open file
mris_anatomical_stats: could not read input volume 
/cubric/data/c1749990/freesurfer/subjects/PPT_001/mri/wm.mgz

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From:  on behalf of "Douglas N. Greve" 

Reply to: Freesurfer support list 
Date: Monday, 4 May 2020 at 18:54
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Recon-all exited WITH errors

Unfortunately, the log file does not indicate what went wrong. But it does show 
that the error happened on the LH (so it is not just RH). Run the command below 
and send all terminal output

cd /home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white


On 5/4/2020 1:34 PM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

I appear to be having some issues with recon-all. I ran the command from a bash 
script (see attached), and it appears to work fine for the left hemisphere as 
the correct files are in the surf folder. However, there are no right 
hemisphere surf files. I have attached the log and error log for PPT01 and 
PPT02. Any advice on as to why this has happened would be great.

Thanks in advance,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628




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Re: [Freesurfer] Recon-all exited WITH errors

[Douglas N. Greve]

Unfortunately, the log file does not indicate what went wrong. But it 
does show that the error happened on the LH (so it is not just RH). Run 
the command below and send all terminal output


cd 
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a 
../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab PPT_001 lh white




On 5/4/2020 1:34 PM, Mason Wells wrote:


External Email - Use Caution

Hi Experts,

I appear to be having some issues with recon-all. I ran the command 
from a bash script (see attached), and it appears to work fine for the 
left hemisphere as the correct files are in the surf folder. However, 
there are no right hemisphere surf files. I have attached the log and 
error log for PPT01 and PPT02. Any advice on as to why this has 
happened would be great.


Thanks in advance,

Mason

*Mason T Wells, MSc*

*PhD student*

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK

*/Email/*: wells...@cardiff.ac.uk 

*/Tel/*: 02920 879628

*/Web/*: Cardiff University webpage 





*Mason T Wells, MSc*

*Myfyriwr PhD*

Yr Ysgol Optometreg a Gwyddorau’r Golwg

& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr 
Ysgol Seicoleg


Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU

*/E-bost/*: wells...@caerdydd.ac.uk 

*/Ffôn/*: 02920 879628


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Re: [Freesurfer] Recon-all exited with errors

[Bruce Fischl]

Hi Lily

yes, some brains are harder (and longer to process) than others.

glad it worked out

cheers
Bruce
On Wed, 1 
Apr 2020, Wang, Lily wrote:



Hi Bruce,

I re-ran it without running anything else on the machine. Took almost three 
times as long as my
recons usually take but it finished without error. Thank you for your help!

Best,
Lily

_
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Bruce Fischl 
Sent: Monday, March 30, 2020 5:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all exited with errors  
Hi Lily

that looks ok I think, although it's hard to tell for sure. The
cerebellum shouldn't be included in the surface. Are you sure you have
enough ram on your machine? It looked like half of it was in use when you
ran recon-all. If you want you can tar and gzip the whole subject dir and
ftp it to us and we will take a look, but I would try rerunning when
nothing else is taking up significant chunks of memory on your machine and
see if that fixes it
cheers
Bruce

On Mon, 30 Mar 2020, Wang, Lily wrote:

> Hi Dr. Greve,
>
> I'm not seeing any glaring issues with inclusion of cerebellum or skull in
> the surfaces or the mgz. There is a bit of inclusion of the cerebellum in
> the wm.mgz. However, two things that do seem strange are 1. a portion of the
> subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it
> looks like the ventricles are supposed to be white, but a big portion of
> this subject's ventricles are not included and it seems that it's messing up
> the lh.orig.nofix surface as well. Could this possibly be an issue? Please
> see attached screenshot.
>
> Thank you,
> Lily
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N. Greve
> 
> Sent: Monday, March 30, 2020 11:55 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] Recon-all exited with errors  
> It looks like there might be a very large defect. Try looking at the wm.mgz
> and brainmask.mgz and the lh.orig.nofix surface to see if there is a large
> part of skull or cerebellum that is encompassed in the orig.nofix surface
>
> On 3/30/2020 11:26 AM, Wang, Lily wrote:
>   Hi All,
>
> I have a subject whose T1 quality is quite good but reconstruction
> exited with errors so I am not sure what the issue could be. Attached
> is the recon-all.log. Could it be that the subject is very old and has
> a lot of degeneration?
>
> Thank you,
> Lily
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
>
>

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Re: [Freesurfer] Recon-all exited with errors

[Wang, Lily]

Hi Bruce,

I re-ran it without running anything else on the machine. Took almost three 
times as long as my recons usually take but it finished without error. Thank 
you for your help!

Best,
Lily


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, March 30, 2020 5:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all exited with errors

Hi Lily

that looks ok I think, although it's hard to tell for sure. The
cerebellum shouldn't be included in the surface. Are you sure you have
enough ram on your machine? It looked like half of it was in use when you
ran recon-all. If you want you can tar and gzip the whole subject dir and
ftp it to us and we will take a look, but I would try rerunning when
nothing else is taking up significant chunks of memory on your machine and
see if that fixes it
cheers
Bruce

On Mon, 30 Mar 2020, Wang, Lily wrote:

> Hi Dr. Greve,
>
> I'm not seeing any glaring issues with inclusion of cerebellum or skull in
> the surfaces or the mgz. There is a bit of inclusion of the cerebellum in
> the wm.mgz. However, two things that do seem strange are 1. a portion of the
> subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it
> looks like the ventricles are supposed to be white, but a big portion of
> this subject's ventricles are not included and it seems that it's messing up
> the lh.orig.nofix surface as well. Could this possibly be an issue? Please
> see attached screenshot.
>
> Thank you,
> Lily
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N. Greve
> 
> Sent: Monday, March 30, 2020 11:55 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: Re: [Freesurfer] Recon-all exited with errors
> It looks like there might be a very large defect. Try looking at the wm.mgz
> and brainmask.mgz and the lh.orig.nofix surface to see if there is a large
> part of skull or cerebellum that is encompassed in the orig.nofix surface
>
> On 3/30/2020 11:26 AM, Wang, Lily wrote:
>   Hi All,
>
> I have a subject whose T1 quality is quite good but reconstruction
> exited with errors so I am not sure what the issue could be. Attached
> is the recon-all.log. Could it be that the subject is very old and has
> a lot of degeneration?
>
> Thank you,
> Lily
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
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Re: [Freesurfer] Recon-all exited with errors

[Bruce Fischl]

Hi Lily

that looks ok I think, although it's hard to tell for sure. The 
cerebellum shouldn't be included in the surface. Are you sure you have 
enough ram on your machine? It looked like half of it was in use when you 
ran recon-all. If you want you can tar and gzip the whole subject dir and 
ftp it to us and we will take a look, but I would try rerunning when 
nothing else is taking up significant chunks of memory on your machine and 
see if that fixes it

cheers
Bruce

On Mon, 30 Mar 2020, Wang, Lily wrote:


Hi Dr. Greve,

I'm not seeing any glaring issues with inclusion of cerebellum or skull in
the surfaces or the mgz. There is a bit of inclusion of the cerebellum in
the wm.mgz. However, two things that do seem strange are 1. a portion of the
subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it
looks like the ventricles are supposed to be white, but a big portion of
this subject's ventricles are not included and it seems that it's messing up
the lh.orig.nofix surface as well. Could this possibly be an issue? Please
see attached screenshot.

Thank you,
Lily


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Douglas N. Greve

Sent: Monday, March 30, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Recon-all exited with errors  
It looks like there might be a very large defect. Try looking at the wm.mgz
and brainmask.mgz and the lh.orig.nofix surface to see if there is a large
part of skull or cerebellum that is encompassed in the orig.nofix surface

On 3/30/2020 11:26 AM, Wang, Lily wrote:
  Hi All,

I have a subject whose T1 quality is quite good but reconstruction
exited with errors so I am not sure what the issue could be. Attached
is the recon-all.log. Could it be that the subject is very old and has
a lot of degeneration?

Thank you,
Lily

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Re: [Freesurfer] Recon-all exited with errors

[Wang, Lily]

Hi Dr. Greve,

I'm not seeing any glaring issues with inclusion of cerebellum or skull in the 
surfaces or the mgz. There is a bit of inclusion of the cerebellum in the 
wm.mgz. However, two things that do seem strange are 1. a portion of the 
subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it looks 
like the ventricles are supposed to be white, but a big portion of this 
subject's ventricles are not included and it seems that it's messing up the 
lh.orig.nofix surface as well. Could this possibly be an issue? Please see 
attached screenshot.

Thank you,
Lily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, March 30, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Recon-all exited with errors

It looks like there might be a very large defect. Try looking at the wm.mgz and 
brainmask.mgz and the lh.orig.nofix surface to see if there is a large part of 
skull or cerebellum that is encompassed in the orig.nofix surface

On 3/30/2020 11:26 AM, Wang, Lily wrote:
Hi All,

I have a subject whose T1 quality is quite good but reconstruction exited with 
errors so I am not sure what the issue could be. Attached is the recon-all.log. 
Could it be that the subject is very old and has a lot of degeneration?

Thank you,
Lily



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Re: [Freesurfer] Recon-all exited with errors

[Douglas N. Greve]

It looks like there might be a very large defect. Try looking at the 
wm.mgz and brainmask.mgz and the lh.orig.nofix surface to see if there 
is a large part of skull or cerebellum that is encompassed in the 
orig.nofix surface


On 3/30/2020 11:26 AM, Wang, Lily wrote:

Hi All,

I have a subject whose T1 quality is quite good but reconstruction 
exited with errors so I am not sure what the issue could be. Attached 
is the recon-all.log. Could it be that the subject is very old and has 
a lot of degeneration?


Thank you,
Lily

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Re: [Freesurfer] recon-all exited with ERRORS

[Greve, Douglas N.,Ph.D.]

THe last command run is
ln -s lh.white.preaparc.H lh.white.H
So I'm guessing that the error comes when the symbolic link is created (and it 
would not be captured in recon-all). That link is the first created in the 
stream, so it would not necessarily have  shown itself before then. Try this:
cd /mnt/hgfs/ShareFolder/output/sample01/surf
ln -s lh.white.preaparc.H lh.white.H
Is there an error? If so, sent the error msg


On 8/2/2019 9:57 PM, Kuo Li wrote:

External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to do cortical reconstruction, but for some of my subjects I get 
the following error when I run the recon-all command:

#
#@# Curv .H and .K lh Wed Jul 17 04:03:21 PDT 2019
/mnt/hgfs/ShareFolder/output/sample01/surf

 mris_curvature -w lh.white.preaparc

total integrated curvature = 0.838*4pi (10.527) --> 0 handles
ICI = 216.7, FI = 1989.1, variation=32373.324
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux ubuntu 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27 07:28:31 UTC 
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sample01 exited with ERRORS at Wed Jul 17 04:03:23 PDT 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I've searched google and no similar errors have been reported. Does anyone have 
any thoughts on how to trouble-shoot this one? Also, I've attached the 
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 18.04.2 LTS
3) recon-all -i sample-001.nii.gz -s sample01 -all
4) recon-all.log: see attached




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Re: [Freesurfer] recon-all exited with ERRORS

[Bruce Fischl]

hmmm, what system are you running on in terms of software and hardware? I 
don't see any errors in the log file so I'm not sure why it stopped. You 
should be able to rerun these subjects with -make all to complete them


cheers
Bruce
On 
Sat, 3 Aug 2019, Kuo Li wrote:




External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to do cortical reconstruction, but for some of my subjects I
get the following error when I run the recon-all command:
 
#
#@# Curv .H and .K lh Wed Jul 17 04:03:21 PDT 2019
/mnt/hgfs/ShareFolder/output/sample01/surf

 mris_curvature -w lh.white.preaparc

total integrated curvature = 0.838*4pi (10.527) --> 0 handles
ICI = 216.7, FI = 1989.1, variation=32373.324
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
Linux ubuntu 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27 07:28:31
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sample01 exited with ERRORS at Wed Jul 17 04:03:23 PDT 2019

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I've searched google and no similar errors have been reported. Does anyone
have any thoughts on how to trouble-shoot this one? Also, I've attached the
recon-all.log in case it's of any use.

1) FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 18.04.2 LTS
3) recon-all -i sample-001.nii.gz -s sample01 -all
4) recon-all.log: see attached


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Re: [Freesurfer] Recon-all exited with errors

[Bruce Fischl]

thanks Rob
Bruce
On Tue, 19 Jun 2018, Dicamillo, Robert wrote:


I followed up with Ryan off the list one this one yesterday, i.e., he tried one 
of the
later dev builds which fixes those lib issues.  I think recon-all runs for him 
now w/o
the lib errors, but
he is getting a non-zero exit from something else.

- rob

  On Jun 19, 2018, at 11:00 AM, Hoopes, Andrew 
  wrote:

Hi Ryan, this issue should be fixed in the freesurfer development version, but 
as
a temporary fix to get things working in v6, I would suggest disabling SIP and
rerunning:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best
Andrew
 
 
From:  on behalf of Ryan Flores

Reply-To: FS Help 
Date: Monday, June 18, 2018 at 1:07 PM
To: FS Help 
Subject: [Freesurfer] Recon-all exited with errors
 

External Email - Use Caution

Dear FS developers,
 
I tried running recon-all using the -parallel flag over the weekend, but to my
surprise they all exited with errors. I’m hoping the problem is something 
subtle,
but I’m having trouble understanding the error log (please see attached). Can
someone point out the issue? Thank you for your help.
 
Best,
 
Ryan
 
-- 
Ryan Flores
Clinical Research Coordinator
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Recon-all exited with errors

[Dicamillo, Robert]

I followed up with Ryan off the list one this one yesterday, i.e., he tried one 
of the later dev
builds which fixes those lib issues.  I think recon-all runs for him now w/o 
the lib errors, but
he is getting a non-zero exit from something else.

- rob

On Jun 19, 2018, at 11:00 AM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:

Hi Ryan, this issue should be fixed in the freesurfer development version, but 
as a temporary fix to get things working in v6, I would suggest disabling SIP 
and rerunning:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best
Andrew


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Ryan Flores mailto:rya...@stanford.edu>>
Reply-To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, June 18, 2018 at 1:07 PM
To: FS Help 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Recon-all exited with errors


External Email - Use Caution

Dear FS developers,

I tried running recon-all using the -parallel flag over the weekend, but to my 
surprise they all exited with errors. I’m hoping the problem is something 
subtle, but I’m having trouble understanding the error log (please see 
attached). Can someone point out the issue? Thank you for your help.

Best,

Ryan

--
Ryan Flores
Clinical Research Coordinator
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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

[Hoopes, Andrew]

Hi Ryan, this issue should be fixed in the freesurfer development version, but 
as a temporary fix to get things working in v6, I would suggest disabling SIP 
and rerunning:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
best
Andrew


From:  on behalf of Ryan Flores 

Reply-To: FS Help 
Date: Monday, June 18, 2018 at 1:07 PM
To: FS Help 
Subject: [Freesurfer] Recon-all exited with errors


External Email - Use Caution
Dear FS developers,

I tried running recon-all using the -parallel flag over the weekend, but to my 
surprise they all exited with errors. I’m hoping the problem is something 
subtle, but I’m having trouble understanding the error log (please see 
attached). Can someone point out the issue? Thank you for your help.

Best,

Ryan

--
Ryan Flores
Clinical Research Coordinator
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Re: [Freesurfer] Recon-all exited with errors

[Hanna Vasilevskaya]

External Email - Use Caution

Thank you for your reply!


Here is an exempt from the terminal from one of the subjects. This is how it 
ended:



#@# Curv .H and .K lh Tue Jun  5 16:06:08 DST 2018
/mnt/d/Freesurfer_CTE/1062_2/surf

 mris_curvature -w lh.white.preaparc

total integrated curvature = 5.493*4pi (69.027) --> -4 handles
ICI = 150.0, FI = 1629.4, variation=25419.408
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not permitted
Linux Laptop 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST 2014 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 1062_2 exited with ERRORS at Tue Jun  5 16:06:13 DST 2018



Thank you!

Anna


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, June 4, 2018 6:11:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all exited with errors

It is not clear what the actual error is. Is there anything that gets
printed out to the terminal that is not in the log? Also, can you verify
that the disk is not filling up?


On 06/04/2018 04:53 PM, Hanna Vasilevskaya wrote:
>
>
> Good afternoon all,
>
>
> I am new to Freesurfer (using version 6.0) and trying to run recon-all
> on multiple subjects. Every subject exited with errors. Specifically,
> a number of surfaces are missing from the "surf" subject's folder
> (only 30 files instead of 80). Would you happen to know how to fix it?
>
>
> Taken from the recon-all status log:
>
> #@# Smooth2 lh Mon Jun  4 16:26:27 DST 2018
> #@# Smooth2 rh Mon Jun  4 16:26:31 DST 2018
> #@# Inflation2 lh Mon Jun  4 16:26:35 DST 2018
> #@# Inflation2 rh Mon Jun  4 16:27:02 DST 2018
> #@# Curv .H and .K lh Mon Jun  4 16:27:29 DST 2018
> Linux Laptop 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST
> 2014 x86_64 x86_64 x86_64 GNU/Linux
> recon-all -s 1062_2 exited with ERRORS at Mon Jun  4 16:27:32 DST 2018
>
> I have also attached a recon-all.log for your convenience.
>
> Thank you,
> Anna
>
>
>
>
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Re: [Freesurfer] Recon-all exited with errors

[Douglas N. Greve]

It is not clear what the actual error is. Is there anything that gets 
printed out to the terminal that is not in the log? Also, can you verify 
that the disk is not filling up?


On 06/04/2018 04:53 PM, Hanna Vasilevskaya wrote:
>
>
> Good afternoon all,
>
>
> I am new to Freesurfer (using version 6.0) and trying to run recon-all 
> on multiple subjects. Every subject exited with errors. Specifically, 
> a number of surfaces are missing from the "surf" subject's folder 
> (only 30 files instead of 80). Would you happen to know how to fix it?
>
>
> Taken from the recon-all status log:
>
> #@# Smooth2 lh Mon Jun  4 16:26:27 DST 2018
> #@# Smooth2 rh Mon Jun  4 16:26:31 DST 2018
> #@# Inflation2 lh Mon Jun  4 16:26:35 DST 2018
> #@# Inflation2 rh Mon Jun  4 16:27:02 DST 2018
> #@# Curv .H and .K lh Mon Jun  4 16:27:29 DST 2018
> Linux Laptop 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST 
> 2014 x86_64 x86_64 x86_64 GNU/Linux
> recon-all -s 1062_2 exited with ERRORS at Mon Jun  4 16:27:32 DST 2018
>
> I have also attached a recon-all.log for your convenience.
>
> Thank you,
> Anna
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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
> 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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but does not contain patient information, please contact the sender and properly
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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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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,

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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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]

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
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)

[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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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
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 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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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
>>
>>
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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
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> 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
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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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Re: [Freesurfer] recon-all exited with ERRORS

[Douglas N Greve]

What edits did you make to it? Can you check the T1.mgz to see if it 
looks ok?


On 02/15/2017 07:56 AM, Dayanne Ferreira Ayres wrote:
> Good morning, I tried to process a patient with the command below 
> after editing it:
>
> Recon-all-all -sd / Applications / freesurfer / subjects -no-isrunning 
> -subjid ArlindoRibeirodaSilvaFilhoADRIANO_2009
>
> The file with the error log follows in the attachment.
>
> Freesurfer version: 5.3
> Platform: MAC OS X yosemite, version 10.10
>
>
> Att, Dayanne Ayres
>
>
> ___
> 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/

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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

[Z K]

Yes, that would be a good option. Its a little work but here is a guide 
that I dug up which helps explain the process. For the version of linux 
to use... I would recommend Ubuntu 14.04.5 LTS 
(https://www.ubuntu.com/download/alternative-downloads)



On 10/13/2016 01:25 PM, Brad Matushewski wrote:
> Would a feasible approach be to set up a dual-boot on my PC so that I can 
> boot directly into either a Windows or Linux environment?
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
> Sent: Thursday, October 13, 2016 12:53 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
> I was afraid this was the case. Normally in this situation I would say set up 
> a shared folder between the host and the virtual machines. But unfortunately 
> there is a known bug in the the MNI tools shipped with freesurfer which makes 
> this an incompatible arrangement.
>
> The disk space was assigned to allow perhaps a few subjects worth of data 
> onto the virtual image, otherwise the download size would have been 
> prohibitively large. If you want to process numerous subjects the VirtualBox 
> version is insuffiecient, you will have to use the Mac or Linux version.
>
>
> On 10/13/2016 12:39 PM, Brad Matushewski wrote:
>> I would appear that the allotted hard drive space is fixed as a function of 
>> the Freesurfer installation.  There does not appear to be an option to 
>> expand allotted space either at time of installation or after the fact.
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
>> Sent: Thursday, October 13, 2016 11:03 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad
>> Matushewski <bjmat...@uwo.ca>
>> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>>
>>
>> I think its referring to the hard disk space in the virtual machine. You 
>> probably ran out which is not surprising, as the amount of free space 
>> provided with the disk image is fairly small. The fact the your host machine 
>> has 305Gb of HD on the host machine is unknown to the virtual machine.
>>
>> See if you can expand the hard disk space of the virtual machine (not sure 
>> if this is adjustable or not). Also, try setting up a shared folder between 
>> the two (this has other potential issues, but is worth trying).
>>
>> -Zeke
>>
>>
>> On 10/13/2016 10:58 AM, Brad Matushewski wrote:
>>> Thank you, Bruce for the rapid reply.  I am running Freesurfer on a 
>>> (Windows 10 based), virtual machine.  I installed / set it up according to 
>>> the directions posted here:
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirt
>>> u
>>> alImage
>>>
>>> ...specifically referring to the recommended memory suggestions of 4MB.  
>>> Otherwise, I saw no other options for specifying memory requirements.
>>>
>>> What is the nature of this memory error and how do I go about fixing it?  I 
>>> know that I have 305 Gb of HD.
>>>
>>>
>>>
>>>
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
>>> Fischl
>>> Sent: Thursday, October 13, 2016 9:43 AM
>>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>>>
>>> Hi Brad
>>>
>>> it looks like the recon failed as you ran out of disk space:
>>>
>>> cvarput: ncid 5: No space left on device
>>> miicv_put: MINC package entry point
>>> nu_evaluate: crashed while running mincmath (termination status=768)
>>> nu_correct: crashed while running nu_evaluate (termination
>>> status=768)
>>>
>>>
>>> as for what would have been next, that of course depends on what you
>>> want to study
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On
>>> Thu,
>>> 13 Oct
>>> 2016, Brad Matushewski wrote:
>>>
>>>>
>>>>
>>>>
>>>> I just tried to run my first recon-all.
>>>>
>>>>
>>>>
>>>> What now?
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>&g

Re: [Freesurfer] recon-all exited with ERRORS

[Brad Matushewski]

Would a feasible approach be to set up a dual-boot on my PC so that I can boot 
directly into either a Windows or Linux environment?


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13, 2016 12:53 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS

I was afraid this was the case. Normally in this situation I would say set up a 
shared folder between the host and the virtual machines. But unfortunately 
there is a known bug in the the MNI tools shipped with freesurfer which makes 
this an incompatible arrangement.

The disk space was assigned to allow perhaps a few subjects worth of data onto 
the virtual image, otherwise the download size would have been prohibitively 
large. If you want to process numerous subjects the VirtualBox version is 
insuffiecient, you will have to use the Mac or Linux version.


On 10/13/2016 12:39 PM, Brad Matushewski wrote:
> I would appear that the allotted hard drive space is fixed as a function of 
> the Freesurfer installation.  There does not appear to be an option to expand 
> allotted space either at time of installation or after the fact.
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
> Sent: Thursday, October 13, 2016 11:03 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad 
> Matushewski <bjmat...@uwo.ca>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
>
> I think its referring to the hard disk space in the virtual machine. You 
> probably ran out which is not surprising, as the amount of free space 
> provided with the disk image is fairly small. The fact the your host machine 
> has 305Gb of HD on the host machine is unknown to the virtual machine.
>
> See if you can expand the hard disk space of the virtual machine (not sure if 
> this is adjustable or not). Also, try setting up a shared folder between the 
> two (this has other potential issues, but is worth trying).
>
> -Zeke
>
>
> On 10/13/2016 10:58 AM, Brad Matushewski wrote:
>> Thank you, Bruce for the rapid reply.  I am running Freesurfer on a (Windows 
>> 10 based), virtual machine.  I installed / set it up according to the 
>> directions posted here:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirt
>> u
>> alImage
>>
>> ...specifically referring to the recommended memory suggestions of 4MB.  
>> Otherwise, I saw no other options for specifying memory requirements.
>>
>> What is the nature of this memory error and how do I go about fixing it?  I 
>> know that I have 305 Gb of HD.
>>
>>
>>
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
>> Fischl
>> Sent: Thursday, October 13, 2016 9:43 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>>
>> Hi Brad
>>
>> it looks like the recon failed as you ran out of disk space:
>>
>> cvarput: ncid 5: No space left on device
>> miicv_put: MINC package entry point
>> nu_evaluate: crashed while running mincmath (termination status=768)
>> nu_correct: crashed while running nu_evaluate (termination 
>> status=768)
>>
>>
>> as for what would have been next, that of course depends on what you 
>> want to study
>>
>> cheers
>> Bruce
>>
>>
>> On
>> Thu,
>> 13 Oct
>> 2016, Brad Matushewski wrote:
>>
>>>
>>>
>>>
>>> I just tried to run my first recon-all.
>>>
>>>
>>>
>>> What now?
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Logo
>>>
>>> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
>>>
>>> Laboratory for Brain & Heart Health
>>> School of Kinesiology
>>> Western University
>>> Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, 
>>> Canada, N6A 5B9
>>> Tel: (519) 661-2111 x 89066
>>> Fax: (519) 850-2447
>>>
>>>
>>>
>>>
>>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

Re: [Freesurfer] recon-all exited with ERRORS

[Z K]

I was afraid this was the case. Normally in this situation I would say 
set up a shared folder between the host and the virtual machines. But 
unfortunately there is a known bug in the the MNI tools shipped with 
freesurfer which makes this an incompatible arrangement.

The disk space was assigned to allow perhaps a few subjects worth of 
data onto the virtual image, otherwise the download size would have been 
prohibitively large. If you want to process numerous subjects the 
VirtualBox version is insuffiecient, you will have to use the Mac or 
Linux version.


On 10/13/2016 12:39 PM, Brad Matushewski wrote:
> I would appear that the allotted hard drive space is fixed as a function of 
> the Freesurfer installation.  There does not appear to be an option to expand 
> allotted space either at time of installation or after the fact.
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
> Sent: Thursday, October 13, 2016 11:03 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad 
> Matushewski <bjmat...@uwo.ca>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
>
> I think its referring to the hard disk space in the virtual machine. You 
> probably ran out which is not surprising, as the amount of free space 
> provided with the disk image is fairly small. The fact the your host machine 
> has 305Gb of HD on the host machine is unknown to the virtual machine.
>
> See if you can expand the hard disk space of the virtual machine (not sure if 
> this is adjustable or not). Also, try setting up a shared folder between the 
> two (this has other potential issues, but is worth trying).
>
> -Zeke
>
>
> On 10/13/2016 10:58 AM, Brad Matushewski wrote:
>> Thank you, Bruce for the rapid reply.  I am running Freesurfer on a (Windows 
>> 10 based), virtual machine.  I installed / set it up according to the 
>> directions posted here:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtu
>> alImage
>>
>> ...specifically referring to the recommended memory suggestions of 4MB.  
>> Otherwise, I saw no other options for specifying memory requirements.
>>
>> What is the nature of this memory error and how do I go about fixing it?  I 
>> know that I have 305 Gb of HD.
>>
>>
>>
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce
>> Fischl
>> Sent: Thursday, October 13, 2016 9:43 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>>
>> Hi Brad
>>
>> it looks like the recon failed as you ran out of disk space:
>>
>> cvarput: ncid 5: No space left on device
>> miicv_put: MINC package entry point
>> nu_evaluate: crashed while running mincmath (termination status=768)
>> nu_correct: crashed while running nu_evaluate (termination status=768)
>>
>>
>> as for what would have been next, that of course depends on what you
>> want to study
>>
>> cheers
>> Bruce
>>
>>
>> On
>> Thu,
>> 13 Oct
>> 2016, Brad Matushewski wrote:
>>
>>>
>>>
>>>
>>> I just tried to run my first recon-all.
>>>
>>>
>>>
>>> What now?
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Logo
>>>
>>> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
>>>
>>> Laboratory for Brain & Heart Health
>>> School of Kinesiology
>>> Western University
>>> Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON,
>>> Canada, N6A 5B9
>>> Tel: (519) 661-2111 x 89066
>>> Fax: (519) 850-2447
>>>
>>>
>>>
>>>
>>>
>>
>> ___
>> 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
>
>
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Re: [Freesurfer] recon-all exited with ERRORS

[Brad Matushewski]

I would appear that the allotted hard drive space is fixed as a function of the 
Freesurfer installation.  There does not appear to be an option to expand 
allotted space either at time of installation or after the fact.


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13, 2016 11:03 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad Matushewski 
<bjmat...@uwo.ca>
Subject: Re: [Freesurfer] recon-all exited with ERRORS


I think its referring to the hard disk space in the virtual machine. You 
probably ran out which is not surprising, as the amount of free space provided 
with the disk image is fairly small. The fact the your host machine has 305Gb 
of HD on the host machine is unknown to the virtual machine.

See if you can expand the hard disk space of the virtual machine (not sure if 
this is adjustable or not). Also, try setting up a shared folder between the 
two (this has other potential issues, but is worth trying).

-Zeke


On 10/13/2016 10:58 AM, Brad Matushewski wrote:
> Thank you, Bruce for the rapid reply.  I am running Freesurfer on a (Windows 
> 10 based), virtual machine.  I installed / set it up according to the 
> directions posted here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtu
> alImage
>
> ...specifically referring to the recommended memory suggestions of 4MB.  
> Otherwise, I saw no other options for specifying memory requirements.
>
> What is the nature of this memory error and how do I go about fixing it?  I 
> know that I have 305 Gb of HD.
>
>
>
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Thursday, October 13, 2016 9:43 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
> Hi Brad
>
> it looks like the recon failed as you ran out of disk space:
>
> cvarput: ncid 5: No space left on device
> miicv_put: MINC package entry point
> nu_evaluate: crashed while running mincmath (termination status=768)
> nu_correct: crashed while running nu_evaluate (termination status=768)
>
>
> as for what would have been next, that of course depends on what you 
> want to study
>
> cheers
> Bruce
>
>
> On
> Thu,
> 13 Oct
> 2016, Brad Matushewski wrote:
>
>>
>>
>>
>> I just tried to run my first recon-all.
>>
>>
>>
>> What now?
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Logo
>>
>> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
>>
>> Laboratory for Brain & Heart Health
>> School of Kinesiology
>> Western University
>> Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, 
>> Canada, N6A 5B9
>> Tel: (519) 661-2111 x 89066
>> Fax: (519) 850-2447
>>
>>
>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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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 
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Re: [Freesurfer] recon-all exited with ERRORS

[Brad Matushewski]

Under Storage: Controller: SATA
Virtual Size: 20Gb
Actual Size: 17.35 Gb

Is there a way to expand this or do I have to delete and reinstall the virtual 
machine?



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13, 2016 11:03 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad Matushewski 
<bjmat...@uwo.ca>
Subject: Re: [Freesurfer] recon-all exited with ERRORS


I think its referring to the hard disk space in the virtual machine. You 
probably ran out which is not surprising, as the amount of free space provided 
with the disk image is fairly small. The fact the your host machine has 305Gb 
of HD on the host machine is unknown to the virtual machine.

See if you can expand the hard disk space of the virtual machine (not sure if 
this is adjustable or not). Also, try setting up a shared folder between the 
two (this has other potential issues, but is worth trying).

-Zeke


On 10/13/2016 10:58 AM, Brad Matushewski wrote:
> Thank you, Bruce for the rapid reply.  I am running Freesurfer on a (Windows 
> 10 based), virtual machine.  I installed / set it up according to the 
> directions posted here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtu
> alImage
>
> ...specifically referring to the recommended memory suggestions of 4MB.  
> Otherwise, I saw no other options for specifying memory requirements.
>
> What is the nature of this memory error and how do I go about fixing it?  I 
> know that I have 305 Gb of HD.
>
>
>
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce 
> Fischl
> Sent: Thursday, October 13, 2016 9:43 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
> Hi Brad
>
> it looks like the recon failed as you ran out of disk space:
>
> cvarput: ncid 5: No space left on device
> miicv_put: MINC package entry point
> nu_evaluate: crashed while running mincmath (termination status=768)
> nu_correct: crashed while running nu_evaluate (termination status=768)
>
>
> as for what would have been next, that of course depends on what you 
> want to study
>
> cheers
> Bruce
>
>
> On
> Thu,
> 13 Oct
> 2016, Brad Matushewski wrote:
>
>>
>>
>>
>> I just tried to run my first recon-all.
>>
>>
>>
>> What now?
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Logo
>>
>> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
>>
>> Laboratory for Brain & Heart Health
>> School of Kinesiology
>> Western University
>> Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, 
>> Canada, N6A 5B9
>> Tel: (519) 661-2111 x 89066
>> Fax: (519) 850-2447
>>
>>
>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Partners Compliance HelpLine 
at http://www.partners.org/complianceline . If the e-mail was sent to you in 
error but does not contain patient information, please contact the sender and 
properly dispose of the e-mail.


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Re: [Freesurfer] recon-all exited with ERRORS

[Z K]

I think its referring to the hard disk space in the virtual machine. You 
probably ran out which is not surprising, as the amount of free space 
provided with the disk image is fairly small. The fact the your host 
machine has 305Gb of HD on the host machine is unknown to the virtual 
machine.

See if you can expand the hard disk space of the virtual machine (not 
sure if this is adjustable or not). Also, try setting up a shared folder 
between the two (this has other potential issues, but is worth trying).

-Zeke


On 10/13/2016 10:58 AM, Brad Matushewski wrote:
> Thank you, Bruce for the rapid reply.  I am running Freesurfer on a (Windows 
> 10 based), virtual machine.  I installed / set it up according to the 
> directions posted here:
> https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage
>
> ...specifically referring to the recommended memory suggestions of 4MB.  
> Otherwise, I saw no other options for specifying memory requirements.
>
> What is the nature of this memory error and how do I go about fixing it?  I 
> know that I have 305 Gb of HD.
>
>
>
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, October 13, 2016 9:43 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
> Hi Brad
>
> it looks like the recon failed as you ran out of disk space:
>
> cvarput: ncid 5: No space left on device
> miicv_put: MINC package entry point
> nu_evaluate: crashed while running mincmath (termination status=768)
> nu_correct: crashed while running nu_evaluate (termination status=768)
>
>
> as for what would have been next, that of course depends on what you want to 
> study
>
> cheers
> Bruce
>
>
> On
> Thu,
> 13 Oct
> 2016, Brad Matushewski wrote:
>
>>
>>
>>
>> I just tried to run my first recon-all.
>>
>>
>>
>> What now?
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Logo
>>
>> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
>>
>> Laboratory for Brain & Heart Health
>> School of Kinesiology
>> Western University
>> Room 402, Arthur & Sonia Labatt Health Sciences Building
>> London, ON, Canada, N6A 5B9
>> Tel: (519) 661-2111 x 89066
>> Fax: (519) 850-2447
>>
>>
>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
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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

[Bruce Fischl]

Hi Brad

how much disk space do you have free? It looks like not enough as the 
message I posted typically means you have run out of space on the sdisk


cheers
Bruce
On 
Thu, 13 Oct 2016, Brad Matushewski wrote:



Thank you, Bruce for the rapid reply.  I am running Freesurfer on a (Windows 10 
based), virtual machine.  I installed / set it up according to the directions 
posted here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage

...specifically referring to the recommended memory suggestions of 4MB.  
Otherwise, I saw no other options for specifying memory requirements.

What is the nature of this memory error and how do I go about fixing it?  I 
know that I have 305 Gb of HD.





-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, October 13, 2016 9:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS

Hi Brad

it looks like the recon failed as you ran out of disk space:

cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_evaluate: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)


as for what would have been next, that of course depends on what you want to 
study

cheers
Bruce


On
Thu,
13 Oct
2016, Brad Matushewski wrote:



 

I just tried to run my first recon-all. 

 

What now?

 

 

 

 

 

Logo

Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.

Laboratory for Brain & Heart Health
School of Kinesiology
Western University
Room 402, Arthur & Sonia Labatt Health Sciences Building
London, ON, Canada, N6A 5B9
Tel: (519) 661-2111 x 89066
Fax: (519) 850-2447

 





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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

[Brad Matushewski]

Thank you, Bruce for the rapid reply.  I am running Freesurfer on a (Windows 10 
based), virtual machine.  I installed / set it up according to the directions 
posted here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage

...specifically referring to the recommended memory suggestions of 4MB.  
Otherwise, I saw no other options for specifying memory requirements.  

What is the nature of this memory error and how do I go about fixing it?  I 
know that I have 305 Gb of HD.





-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, October 13, 2016 9:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS

Hi Brad

it looks like the recon failed as you ran out of disk space:

cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_evaluate: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)


as for what would have been next, that of course depends on what you want to 
study

cheers
Bruce


On
Thu,
13 Oct
2016, Brad Matushewski wrote:

> 
>  
> 
> I just tried to run my first recon-all. 
> 
>  
> 
> What now?
> 
>  
> 
>  
> 
>  
> 
>  
> 
>  
> 
> Logo
> 
> Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
> 
> Laboratory for Brain & Heart Health
> School of Kinesiology
> Western University
> Room 402, Arthur & Sonia Labatt Health Sciences Building
> London, ON, Canada, N6A 5B9
> Tel: (519) 661-2111 x 89066
> Fax: (519) 850-2447
> 
>  
> 
> 
>

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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

[Bruce Fischl]

Hi Brad

it looks like the recon failed as you ran out of disk space:

cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_evaluate: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)


as for what would have been next, that of course depends on what you want 
to study


cheers
Bruce


On 
Thu, 
13 Oct 
2016, Brad Matushewski wrote:




 

I just tried to run my first recon-all. 

 

What now?

 

 

 

 

 

Logo

Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.

Laboratory for Brain & Heart Health
School of Kinesiology
Western University
Room 402, Arthur & Sonia Labatt Health Sciences Building
London, ON, Canada, N6A 5B9
Tel: (519) 661-2111 x 89066
Fax: (519) 850-2447

 


___
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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] recon-all exited with errors

[Fujiwara, Hisako]

Thank you, Zeke for your help! 

Best wishes,
Hisako

-Original Message-
From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] 
Sent: Tuesday, August 04, 2015 4:08 PM
To: Freesurfer support list; Fujiwara, Hisako
Subject: Re: [Freesurfer] recon-all exited with errors

Hello Hisako,

This is a recently discovered bug either mni related or VirtualBox related. The 
issue is that the mri_nu_correct.mni command will fail when executed in the 
VirtualBox environment on a subject whose data exists on a shared folder 
between the host and the virtual machine.

Currently, the only known solution is to import the subject data folder into 
the VirtualBox environment, and then run recon-all.

-Zeke

On 08/04/2015 11:19 AM, Fujiwara, Hisako wrote:
 Hello,

 I am very new to freesurfer who have been using SPM and FSL, and just 
 started doing individual subject analysis. I already had an error 
 message on recon-all step.

 I am using:

 Vertualbox, OS is RedHat 64-bit

 I am using bash (I prefer to do so) so I am not in tsch shell.

 The recon-all process was terminated with error but not sure exactly 
 what the error was even I looked at the recon-all.log file which is 
 attached to this e-mail. According to the line of script, there should 
 be a file called 'talairach.xfm in /mri/transforms folder but I see 
 only the folder called 'bak' which is empty.

 Please advise what is the exact error is and how to solve this problem.

 Thank you so much for your help in advance.

 Hisako

 *

 fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ recon-all 
 -i CAE_2_1_T1.nii -subject CAE_2_1 -all

 WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 INFO: SUBJECTS_DIR is /media/sf_shared_folder

 Actual FREESURFER_HOME /usr/local/freesurfer

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

 /media/sf_shared_folder/CAE_2_1

 mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii
 /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz

 mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii
 /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz

 INFO: using NIfTI-1 qform

 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

 reading from /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii...

 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

 i_ras = (0, -1, 0)

 j_ras = (0, 0, -1)

 k_ras = (1, 0, 0)

 writing to /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz...

 #

 #@# MotionCor Tue Aug  4 10:04:50 EDT 2015

 Found 1 runs

 /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz

 Checking for (invalid) multi-frame inputs...

 WARNING: only one run found. This is OK, but motion

 correction cannot be performed on one run, so I'll

 copy the run to rawavg and continue.

 cp /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz
 /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz

 /media/sf_shared_folder/CAE_2_1

 mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform

 mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform

 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

 reading from /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz...

 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

 i_ras = (0, -1, 0)

 j_ras = (0, 0, -1)

 k_ras = (1, 0, 0)

 Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) 
 voxels.

 Data is conformed to 1 mm size and 256 voxels for all directions

 changing data type from float to uchar (noscale = 0)...

 MRIchangeType: Building histogram

 Reslicing using trilinear interpolation

 writing to /media/sf_shared_folder/CAE_2_1/mri/orig.mgz...

 mri_add_xform_to_header -c
 /media/sf_shared_folder/CAE_2_1/mri/transforms/talairach.xfm
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz

 INFO: extension is mgz

 #

 #@# Talairach Tue Aug  4 10:05:06 EDT 2015

 /media/sf_shared_folder/CAE_2_1/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
 --i orig.mgz --o orig_nu.mgz

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

 recon-all -s CAE_2_1 exited with ERRORS at Tue Aug  4 10:05:13 EDT 
 2015

 For more details, see the log file
 /media/sf_shared_folder/CAE_2_1/scripts/recon-all.log

 To report a problem, see
 https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.har
 vard.edu_fswiki_BugReportingd=BQIF-gc=P0c35rBvlN7D8BNx7kSJTgr=irT_w
 sJtD80udNn2jMvx1MUsr-k7TAFC5R4iJrY-rOAm=CNRhBZT-7el4JHrXWT1pMkcCxTr7n
 AiwdW0KqdCmL-0s=77s99nYShDEQhOUBas6lQvd60QUPBdrcqJYMzY93ExMe=

 fsuser@xubuntu-VirtualBox:/media

Re: [Freesurfer] recon-all exited with errors

[Z K]

Hello Hisako,

This is a recently discovered bug either mni related or VirtualBox 
related. The issue is that the mri_nu_correct.mni command will fail 
when executed in the VirtualBox environment on a subject whose data 
exists on a shared folder between the host and the virtual machine.

Currently, the only known solution is to import the subject data folder 
into the VirtualBox environment, and then run recon-all.

-Zeke

On 08/04/2015 11:19 AM, Fujiwara, Hisako wrote:
 Hello,

 I am very new to freesurfer who have been using SPM and FSL, and just
 started doing individual subject analysis. I already had an error
 message on recon-all step.

 I am using:

 Vertualbox, OS is RedHat 64-bit

 I am using bash (I prefer to do so) so I am not in tsch shell.

 The recon-all process was terminated with error but not sure exactly
 what the error was even I looked at the recon-all.log file which is
 attached to this e-mail. According to the line of script, there should
 be a file called ‘talairach.xfm in /mri/transforms folder but I see only
 the folder called ‘bak’ which is empty.

 Please advise what is the exact error is and how to solve this problem.

 Thank you so much for your help in advance.

 Hisako

 *

 fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ recon-all -i
 CAE_2_1_T1.nii -subject CAE_2_1 -all

 WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 INFO: SUBJECTS_DIR is /media/sf_shared_folder

 Actual FREESURFER_HOME /usr/local/freesurfer

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

 /media/sf_shared_folder/CAE_2_1

 mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii
 /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz

 mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii
 /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz

 INFO: using NIfTI-1 qform

 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

 reading from /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii...

 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

 i_ras = (0, -1, 0)

 j_ras = (0, 0, -1)

 k_ras = (1, 0, 0)

 writing to /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz...

 #

 #@# MotionCor Tue Aug  4 10:04:50 EDT 2015

 Found 1 runs

 /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz

 Checking for (invalid) multi-frame inputs...

 WARNING: only one run found. This is OK, but motion

 correction cannot be performed on one run, so I'll

 copy the run to rawavg and continue.

 cp /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz
 /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz

 /media/sf_shared_folder/CAE_2_1

 mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform

 mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform

 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

 reading from /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz...

 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

 i_ras = (0, -1, 0)

 j_ras = (0, 0, -1)

 k_ras = (1, 0, 0)

 Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180)
 voxels.

 Data is conformed to 1 mm size and 256 voxels for all directions

 changing data type from float to uchar (noscale = 0)...

 MRIchangeType: Building histogram

 Reslicing using trilinear interpolation

 writing to /media/sf_shared_folder/CAE_2_1/mri/orig.mgz...

 mri_add_xform_to_header -c
 /media/sf_shared_folder/CAE_2_1/mri/transforms/talairach.xfm
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz
 /media/sf_shared_folder/CAE_2_1/mri/orig.mgz

 INFO: extension is mgz

 #

 #@# Talairach Tue Aug  4 10:05:06 EDT 2015

 /media/sf_shared_folder/CAE_2_1/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
 --i orig.mgz --o orig_nu.mgz

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

 recon-all -s CAE_2_1 exited with ERRORS at Tue Aug  4 10:05:13 EDT 2015

 For more details, see the log file
 /media/sf_shared_folder/CAE_2_1/scripts/recon-all.log

 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$



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Re: [Freesurfer] recon-all exited w/errors

[Bruce Fischl]

Hi Katica

what format was the input image to recon-all? Can you verify that tkmedit 
has the directions correct (that is what it labels as anterior is actually 
anatomically anterior, etc...). If so, then the talairach just failed and 
you will need to either try an alternative (like the MNI or SPM talairachs) 
or generate it manually.


cheers
Bruce



On Thu, 2 Jan 2014, Boric, Katica A. 
wrote:



Happy New Year freesuerfers!
I run into this error while doing recon-all :

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0.  threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.

I would really appreciate if someone could give me some advice on how to fix
this error.

Thank you very much!

Katica Boric,


ps: Here is the error log:

#@# Talairach Failure Detection Thu Jan  2 14:20:32 EST 2014
/home/XX/XXX/subjects/XXX_SurferOutput/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0.  threshold=0.0050)
INFO: Attempting MINC mritotal to perform Talairach align
#
#@# Talairach Thu Jan  2 14:20:33 EST 2014
/home/XX/XXX/subjects/XXX_SurferOutput/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz 


 talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

/home/XX/XXX/subjects/XXX_SurferOutput/mri
/usr/local/freesurfer/bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $
Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Thu Jan  2 14:21:30 EST 2014
tmpdir is transforms/tmp.talairach.34005
/home/XX/XXX/subjects/XXX_SurferOutput/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.34005/src.mnc 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=8.23, TE=3.22, TI=450.00, flip angle=12.00
i_ras = (-1, -9.03383e-08, 0)
j_ras = (-1.3411e-07, 2.66591e-08, -1)
k_ras = (1.59256e-07, 1, -5.93718e-09)
writing to transforms/tmp.talairach.34005/src.mnc...

mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.34005/src.mnc transforms/talairach.auto.xfm
Legacy library shellwords.pl will be removed from the Perl core distribution
in the next major release. Please install it from the CPAN distribution
Perl4::CoreLibs. It is being used at /usr/local/freesurfer/mni/bin/mritotal,
line 460.
 
 
Thu Jan  2 14:21:43 EST 2014
talairach done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#
#@# Talairach Failure Detection Thu Jan  2 14:21:44 EST 2014
/home/XX/XXX/subjects/XXX_SurferOutput/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0.  threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42
UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s xxx_SurferOutput exited with ERRORS at Thu Jan  2 14:21:45 EST
2014





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Re: [Freesurfer] recon-all exited with errors

[Douglas N Greve]

Hi Luzia, do you have permission to see that file? Can you send the 
recon-all.log file?
doug


On 09/03/2013 07:32 AM, Troebinger, Luzia wrote:
 Hi all,

 I posted a message regarding this problem a while ago, but still not 
 resolved. Basically, freesurfer exits with errors in the final 
 (autorecon-3) stages, because of what must be a problem with the 
 symbolic link lh.EC_average. The link is created as should be, but I 
 get an error message saying the file lh.EC_average/surf/lh.sphere.reg 
 doesn't exist. I checked that the path to the subjects directory is 
 correct, and that the file in question exists, and both was the case. 
 I am running out of ideas of how to fix this - does anyone know what 
 might be going wrong?

 Best
 Luzia


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Re: [Freesurfer] recon-all exited with ERRORS

[Douglas N Greve]

Can you send the recon-all.log file?

Zhangyuanchao wrote:
 Dear expert，
 We compute the MRI data with FREESURFER using 
  instruction recon-all -s   -all,but some data will  show  recon 
 -all exited with ERRORS  in the recon-all-status.log. The flowing 
 display error information :
 status file for recon-all
 Thu Nov 11 19:22:13 HKT 2010
 recon-all finished without error at Thu Nov 11 19:22:17 HKT 2010



 New invocation of recon-all 



 status file for recon-all
 Thu Nov 11 20:26:17 HKT 2010
 #...@# MotionCor Thu Nov 11 20:26:17 HKT 2010
 #...@# Nu Intensity Correction Thu Nov 11 20:26:33 HKT 2010
 #...@# Talairach Thu Nov 11 20:26:57 HKT 2010
 #...@# Talairach Failure Detection Thu Nov 11 20:27:50 HKT 2010
 #...@# Intensity Normalization Thu Nov 11 20:27:50 HKT 2010
 #...@# Skull Stripping Thu Nov 11 20:31:17 HKT 2010
 Linux ccm.web 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 
 2010 x86_64 x86_64 x86_64 GNU/Linux

 recon-all exited with ERRORS at Thu Nov 11 23:17:40 HKT 2010

 OR   

 LIKE THIS:
   

 status file for recon-all
 Thu Nov 11 19:33:11 HKT 2010
 recon-all finished without error at Thu Nov 11 19:33:15 HKT 2010



 New invocation of recon-all 



 status file for recon-all
 Mon Nov 22 00:51:21 HKT 2010
 #...@# MotionCor Mon Nov 22 00:51:21 HKT 2010
 #...@# Nu Intensity Correction Mon Nov 22 00:51:37 HKT 2010
 #...@# Talairach Mon Nov 22 00:52:34 HKT 2010
 #...@# Talairach Failure Detection Mon Nov 22 00:53:20 HKT 2010
 #...@# Intensity Normalization Mon Nov 22 00:53:20 HKT 2010
 #...@# Skull Stripping Mon Nov 22 00:56:37 HKT 2010
 #...@# EM Registration Mon Nov 22 02:36:07 HKT 2010
 #...@# CA Normalize Mon Nov 22 03:17:48 HKT 2010
 #...@# CA Reg Mon Nov 22 03:20:05 HKT 2010
 #...@# CA Reg Inv Mon Nov 22 07:03:03 HKT 2010
 #...@# Remove Neck Mon Nov 22 07:04:31 HKT 2010
 #...@# SkullLTA Mon Nov 22 07:06:08 HKT 2010
 #...@# SubCort Seg Mon Nov 22 08:12:28 HKT 2010
 Linux ccm.web 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 
 2010 x86_64 x86_64 x86_64 GNU/Linux

 recon-all exited with ERRORS at Mon Nov 22 08:35:10 HKT 2010
 *
 *
 Could you explain to me the reason for the problem and could you solve 
 me the problem? I will appreciate your help very much.
  Best regards,
  Liang Gao 
 


  
 

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Re: [Freesurfer] Recon-all exited with ERRORS

[Angie Morales]

Hi,

I'm trying to run the command: recon-all -subjid subname -autorecon1. I'm
getting the an error message during skull stripping and the error log reads
as follows:

#...@# Skull Stripping Wed Oct 28 12:29:47 PDT 2009
/space/raid7/data/london/data/
mri/other/angie/Freesurfer/SUBJECTS_DIR/5003/mri

 mri_em_register -skull nu.mgz
/space/raid/fmri/freesurfer/average/RB_all_withskull_2008-03-26.gca
transforms/talairach_with_skull.lta

aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading
'/space/raid/fmri/freesurfer/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1   using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as  20.2 or  943.7
total sample mean = 92.0 (1443 zeros)

spacing=8, using 3481 sample points, tol=1.00e-05...

register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 -- 126
resetting gm mean[0]: 74 -- 74
input volume #1 is the most T1-like
using real data threshold=14.0
skull bounding box = (51, 40, 26) -- (206, 255, 255)
using (103, 112, 141) as brain centroid...
mean wm in atlas = 126, using box (84,85,113) -- (122, 138,169) to find MRI
wm
before smoothing, mri peak at 109
after smoothing, mri peak at 110, scaling input intensities by 1.145
scaling channel 0 by 1.14545
initial log_p = -19541.4

First Search limited to translation only.

using real data threshold=42.0

Found translation: (-1.1, 1.1, -17.0): log p = -17915.1

Nine parameter search.  iteration 0 nscales = 0 ...

Linux willis 2.6.27.25-0.1-default #1 SMP 2009-07-01 15:37:09 +0200 x86_64
x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Wed Oct 28 14:45:19 PDT 2009

The error log simply states: CMD mri_watershed

Any advice on how to troubleshoot this problem would be greatly appreciated.

Angie
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Re: [Freesurfer] recon-all exited with ERRORS

[Jenni Pacheco]

Hi Annie,

The aparc+aseg has the aseg subcortical labels in the wm regions, and has 
the parcellation labels along the cortex.  This is overlaid on volumes in 
tkmedit.  A description and a snapshot is shown at the bottom of this 
page:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData

Jenni

On Fri, 18 May 2007, Annie Chiu wrote:


Hi Jenni,

Thanks very much for your speedy reply. Before understanding whether I need
aparc+aseg, could you let me know what the file entails?

Thanks again,
Annie

On 5/17/07 5:48 PM, Jenni Pacheco [EMAIL PROTECTED] wrote:


Hi Annie,

I think what's happening is that it's failing in the aparc+aseg step, but
you can verify this by looking at the status log in your subjects
scripts/recon-all-status.log

This step uses some previously generated input to make a new segmentation.
The lh.ribbon.mgz is a newer addition to the recon-all stream, currently
run in autorecon2.  If your data is old it may not have this, and so the
aparc+aseg can not be generated.  You can either survive without the
aparc+aseg if you don't want it, or you can generate the ?h.ribbon.mgz by
running
recon-all -cortribbon -s subjid and then trying recon-all -aparc2aseg -s
subjid

But first, do verify with the status log that this is the step thats
failing!

Jenni

On Thu, 17 May 2007, Chiu, Annie (NIH/NINDS) [F] wrote:


Hello all,

Using the most updated version of freesurfer, I ran autorecon3 on a set of
data obtained with an old version of the software (the first version) and I
obtained the following error message:

Loading rh annotations from
/home/chiuan/freesurfer/subjects/becker2ANNIE/label/rh.aparc.annot
Have color table for lh white annotation
Have color table for rh white annotation
Loading lh ribbon mask from
/home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz
ERROR: loading aseg
/home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz
Linux mushrat.ninds.nih.gov 2.6.9-42.0.2.ELsmp #1 SMP Thu Aug 17 18:00:32 EDT
2006 i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Wed May 16 22:24:13 EDT 2007

Could someone please clarify?

Thanks in advance,
Annie

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Re: [Freesurfer] recon-all exited with ERRORS

[Jenni Pacheco]

Hi Annie,

I think what's happening is that it's failing in the aparc+aseg step, but 
you can verify this by looking at the status log in your subjects 
scripts/recon-all-status.log


This step uses some previously generated input to make a new segmentation. 
The lh.ribbon.mgz is a newer addition to the recon-all stream, currently 
run in autorecon2.  If your data is old it may not have this, and so the 
aparc+aseg can not be generated.  You can either survive without the 
aparc+aseg if you don't want it, or you can generate the ?h.ribbon.mgz by 
running
recon-all -cortribbon -s subjid and then trying recon-all -aparc2aseg -s 
subjid


But first, do verify with the status log that this is the step thats 
failing!


Jenni

On Thu, 17 May 2007, Chiu, Annie (NIH/NINDS) [F] wrote:


Hello all,

Using the most updated version of freesurfer, I ran autorecon3 on a set of data 
obtained with an old version of the software (the first version) and I obtained 
the following error message:

Loading rh annotations from 
/home/chiuan/freesurfer/subjects/becker2ANNIE/label/rh.aparc.annot
Have color table for lh white annotation
Have color table for rh white annotation
Loading lh ribbon mask from 
/home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz
ERROR: loading aseg 
/home/chiuan/freesurfer/subjects/becker2ANNIE/mri/lh.ribbon.mgz
Linux mushrat.ninds.nih.gov 2.6.9-42.0.2.ELsmp #1 SMP Thu Aug 17 18:00:32 EDT 
2006 i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Wed May 16 22:24:13 EDT 2007

Could someone please clarify?

Thanks in advance,
Annie

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Re: [Freesurfer] recon-all exited with errors

[Nick Schmansky]

Chacko,

The error message 'mrisDefectAnalysis : defect xx overlap defect yy'
appears when running v3.0.1 of freesurfer.  That bug was fixed in
v3.0.2.  I suggest updating your version of freesurfer if possible.

Nick


On Mon, 2006-08-14 at 11:46 -0700, Chacko Cherian wrote:
 Hello all,
 
 One of the subjects I was running exited with ERRORS at the autorecon2 stage.
 This is how it exited.
 
 INFO: assuming .mgz format
 $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $
   $Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $
 before topology correction, eno=-62 (nv=111893, nf=223972, ne=335927, g=32)
 using quasi-homeomorphic spherical map to tessellate cortical surface...
 
 Correction of the Topology
 Finding true center and radius of Spherical Surface...done
 Surface centered at (0,0,0) with radius 100.0 in 8 iterations
 marking ambiguous vertices...
 6825 ambiguous faces found in tessellation
 segmenting defects...
defect 7 : 4 vertices have been added to the surface
defect 21 : 13 vertices have been added to the surface
defect 43 : 11 vertices have been added to the surface
defect 44 : 3 vertices have been added to the surface
defect 48 : 5 vertices have been added to the surface
defect 53 : 9 vertices have been added to the surface
total of 45 vertices has been added to the surface
 analyzing defects...
 mrisDefectAnalysis : defect 21 overlap defect 20
 reading input surface 
 /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/surf/lh.qsphere.nofix...
 reading brain volume from brain...
 reading wm segmentation from wm...
 Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 
 i386 GNU/Linux
 
 
 
 I have also attached the recon-all.log file for reference.
 Thanks in advance for your suggestions.
 
 Regards
 
 Chacko Cherian
 Arizona State University.
 
 
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Re: [Freesurfer] recon-all exited with ERRORS

[Nick Schmansky]

libstdc++ is the standard C++ library.  if your Linux has libstdc+
+.so.5, then the rh9 build of freesurfer should be used.  the centos
builds of freesurfer use libstdc++.so.6.  or, libstd++.so.6 can be
downloaded from the web and installed (google 'libstdc++ rpm').


On Wed, 2006-07-26 at 14:38 -0700, Chacko Cherian wrote:
 Hello all,
 
 I was running recon-all for one of my images and this
 happened to be the error that i got.what is
 libstdc++??
 Could someone please clarify,
 
 Thanks in advance
 
 Chacko.
 
 mri_watershed: error while loading shared libraries:
 libstdc++.so.6: cannot
 open shared object file: No such file or directory
 Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005
 i686 unknown unknown
 GNU/Linux
 
 recon-all exited with ERRORS at Wed Jul 26 13:09:41
 MST 2006
 
 
 
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Re: [Freesurfer] recon-all exited with errors

[Bruce Fischl]

hmm, not sure what's going on here as your orig is newer than your 
inflated, which it shouldn't be:


ls -lrt rh.*
-rw-rw-r--  1 nandita nandita 3202384 Jun 29 15:53 rh.orig.nofix
-rw-rw-r--  1 nandita nandita 3202704 Jun 29 15:53 rh.smoothwm.nofix
-rw-rw-r--  1 nandita nandita 3203048 Jun 29 15:57 rh.inflated.nofix
-rw-rw-r--  1 nandita nandita 3203374 Jun 29 16:29 rh.qsphere.nofix
-rw-rw-r--  1 nandita nandita 3203048 Jun 29 16:29 rh.inflated
-rw-rw-r--  1 nandita nandita  533415 Jun 29 16:30 rh.defect_labels
-rw-rw-r--  1 nandita nandita  533415 Jun 29 16:30 rh.defect_chull
-rw-rw-r--  1 nandita nandita  533415 Jun 29 16:30 rh.defect_borders
-rw-rw-r--  1 nandita nandita 4717916 Jun 29 19:39 rh.orig
-rw-rw-r--  1 nandita nandita 3203358 Jul  5 17:49 rh.sphere

try reprocessing it with -all (instead of -autorecon1, etc..) from the 
beginning, as that's the recommended processing stream now (since it rarely 
fails on reasonable data)


Bruce


On Fri, 
7 
Jul 2006, Nandita Shetty wrote:




Hi,
I came across an error in the third stage of reconstruction using
freesurfer. The images,scripts etc are at

space/megraid/42/ACE/PILOTDATA/DATA_PROCESS

The recon log says that recon-all exited with errors and stopped at Surf
Reg rh. I am a new user and was hoping that you could help me out with the
same. Also, I do know that the inflated brain is not ideal but
nevertheless wanted to complete the reconstruction to get a feel of it.
This is what the error log says
MRISreadVertexPosition(smoothwm): could not open file ../surf/rh.smoothwm
MRISreadOriginalProperties: could not read surface file smoo

Thanks in advance for any help in this regard.
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