Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

[Krystal Xiwing Yau]

External Email - Use Caution

Dear FS experts,


I would like to follow up with the matter here - the T1.mgz isn't generated so 
I cannot inspect the image as instructed by the wiki page. I have checked the 
orientation on FreeView but it's correct. Would you please kindly advise?


Thank you so much. It's been grateful to have your guidance and support.


Sincerely,

Krystal


FreeSurfer Version: 7.3.2

OS: Linux on Ubuntu 23.04



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krystal Xiwing Yau 

Sent: 29 April 2024 16:58:18
To: Freesurfer support list
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error


External Email - Use Caution

Dear FS experts,


I am encountering an error when running recon-all. I followed the FAQ 
<https://secure-web.cisco.com/1UCt6p3edZmVlY3vv2VBSKmRgX9p8Xmur_qX9QMrgPbk8pWw9hHbqUAl1LZ_m2e32JfBHVEoBVrUNQvjBq0U3vvtrtjgPoZTjX7UkqLsMktSt6nn2RFU4zp2wd0wdpswqNm6XAl9mk5UJ-1PEUODQnSFar41wBeWSIboTu0lN5gBeRyNoAiCUEA08mjSPuoyXwcECXM_2QBB8tx8EDMX4WoG7o1xLXJBbOOhubNG1AZpDhbgMLaeECRxthEWcFlWJ8lzNAufWmLdKKeuBWvN8XHkoFomG8UPqPs_pZSPStv6BCjQ0hhTDOYaOfyeLOqA3/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUserContributions%2FFAQ%23Q.Help.21Igotthiserrormessage.3A.22mriwatershederror.3AGLOBALregionofthebrainempty.21.22-whatshouldIdo.3F>
 page to rerun the command but still not running through. Would you please 
kindly advise? The log file is attached to this email.


Thank you.


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
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Re: [Freesurfer] [FreeSurfer] recon-all exited with error

[Krystal Xiwing Yau]

External Email - Use Caution

Dear Yujing,


I will be using a different computer and run it again. Thank you!


Best,

Krystal


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: 22 February 2023 23:35:57
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error

Hi Krystal,

Can you try running recon-all without ‘-parallel’ flag?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krystal Xiwing Yau
Sent: Saturday, February 18, 2023 7:45 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error


External Email - Use Caution

Dear Yujing,



Thank you for spotting it out. I have re-run recon-all in the end as to ensure 
all folders were generated in FreeSurfer. However, I still got the same message 
- the two symbolic links existed in "surf" folder, though. Would you please 
kindly advise what the problem is? Enclosed herewith is the recon-all.log for 
your reference.



Thank you very much!



Best regards,

Krystal


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: 17 February 2023 01:47:15
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error

recon-all failed to create the symbolic links. Here are the errors from 
recon-all.log:

rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
ln: failed to create symbolic link 'rh.white.H': Operation not permitted
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K
ln: failed to create symbolic link 'rh.white.K': Operation not permitted


You can go to your subject surf/ directory 
(/home/developer/guest_shared/Sub-139/surf) to check if you can manually create 
the link -
ln -s rh.white.preaparc.H rh.white.H
ln -s rh.white.preaparc.K rh.white.K

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Krystal Xiwing Yau
Sent: Thursday, February 16, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error


External Email - Use Caution

Dear FreeSurfer experts,



I ran the command "recon-all -s Sub-139 -i 139.nii -all -qcache -parallel 
-openmp 6" successfully in the first few hours, and exited with error before 
generating all the output files.  It happened to other subjects, too.  The 
attached file contains the whole processing steps and ended with error.



I have set SUBJECTS_DIR to the shared folder, which was mounted in FreeSurfer 
beforehand. Then, the data for analysis was copied to the Desktop.  I typed in 
the command and it exited with error in the end, though. Would somebody kindly 
advise how to fix it, please? Your help would be highly appreciated!



OS: Windows 11

VM: ubuntu 18


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
___
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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 https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] [FreeSurfer] recon-all exited with error

[Huang, Yujing]

Hi Krystal,

Can you try running recon-all without '-parallel' flag?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krystal Xiwing Yau
Sent: Saturday, February 18, 2023 7:45 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error


External Email - Use Caution

Dear Yujing,



Thank you for spotting it out. I have re-run recon-all in the end as to ensure 
all folders were generated in FreeSurfer. However, I still got the same message 
- the two symbolic links existed in "surf" folder, though. Would you please 
kindly advise what the problem is? Enclosed herewith is the recon-all.log for 
your reference.



Thank you very much!



Best regards,

Krystal


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: 17 February 2023 01:47:15
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error

recon-all failed to create the symbolic links. Here are the errors from 
recon-all.log:

rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
ln: failed to create symbolic link 'rh.white.H': Operation not permitted
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K
ln: failed to create symbolic link 'rh.white.K': Operation not permitted


You can go to your subject surf/ directory 
(/home/developer/guest_shared/Sub-139/surf) to check if you can manually create 
the link -
ln -s rh.white.preaparc.H rh.white.H
ln -s rh.white.preaparc.K rh.white.K

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Krystal Xiwing Yau
Sent: Thursday, February 16, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error


External Email - Use Caution

Dear FreeSurfer experts,



I ran the command "recon-all -s Sub-139 -i 139.nii -all -qcache -parallel 
-openmp 6" successfully in the first few hours, and exited with error before 
generating all the output files.  It happened to other subjects, too.  The 
attached file contains the whole processing steps and ended with error.



I have set SUBJECTS_DIR to the shared folder, which was mounted in FreeSurfer 
beforehand. Then, the data for analysis was copied to the Desktop.  I typed in 
the command and it exited with error in the end, though. Would somebody kindly 
advise how to fix it, please? Your help would be highly appreciated!



OS: Windows 11

VM: ubuntu 18


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
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] [FreeSurfer] recon-all exited with error

[Huang, Yujing]

recon-all failed to create the symbolic links. Here are the errors from 
recon-all.log:

rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
ln: failed to create symbolic link 'rh.white.H': Operation not permitted
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K
ln: failed to create symbolic link 'rh.white.K': Operation not permitted


You can go to your subject surf/ directory 
(/home/developer/guest_shared/Sub-139/surf) to check if you can manually create 
the link -
ln -s rh.white.preaparc.H rh.white.H
ln -s rh.white.preaparc.K rh.white.K

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Krystal Xiwing Yau
Sent: Thursday, February 16, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error


External Email - Use Caution

Dear FreeSurfer experts,



I ran the command "recon-all -s Sub-139 -i 139.nii -all -qcache -parallel 
-openmp 6" successfully in the first few hours, and exited with error before 
generating all the output files.  It happened to other subjects, too.  The 
attached file contains the whole processing steps and ended with error.



I have set SUBJECTS_DIR to the shared folder, which was mounted in FreeSurfer 
beforehand. Then, the data for analysis was copied to the Desktop.  I typed in 
the command and it exited with error in the end, though. Would somebody kindly 
advise how to fix it, please? Your help would be highly appreciated!



OS: Windows 11

VM: ubuntu 18


Regards,
Krystal

Tel.: +852 2255 5024
Fax: +852 2872 5828
Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.
___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
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 error

[Douglas N. Greve]

You have two inputs, 001.mgz and 002..mgz, and it looks like they have 
different sizes. They must be the same size


On 8/22/2020 3:36 PM, Dalton Bermudez wrote:


External Email - Use Caution

ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
  Currently not supported, maybe first make conform?
  Debug info: size(1) = 1, 1, 1   size(0) = 1, 0.976562, 0.976562
error: No such file or directory
error: MultiRegistration::loadMovables: voxel size is different 
/home/dbermudez/Documents/subjects/00_0001/mri/orig/002.mgz.


However, I have checked the dimensions of both the T1w and the T2w and 
they both have the same dimensions: 176×256×256. I do not know what is 
the problem? and how can I fix the issue?


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[Freesurfer] recon-all exited with error

[Dalton Bermudez]

External Email - Use Caution

ERROR: MultiRegistration::loadMovables: images have different voxel sizes.
  Currently not supported, maybe first make conform?
  Debug info: size(1) = 1, 1, 1   size(0) = 1, 0.976562, 0.976562
error: No such file or directory
error: MultiRegistration::loadMovables: voxel size is different
/home/dbermudez/Documents/subjects/00_0001/mri/orig/002.mgz.

However, I have checked the dimensions of both the T1w and the T2w and they
both have the same dimensions: 176×256×256. I do not know what is the
problem? and how can I fix the issue?
Sat Aug 22 15:19:38 EDT 2020
/home/dbermudez/Documents/subjects/00_0001
/usr/local/freesurfer/bin/recon-all
-all -subjid 00_0001 -i T1w_01_ras.nii -i T2w_01_ras.nii
subjid 00_0001
setenv SUBJECTS_DIR /home/dbermudez/Documents/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-local-build-dev-20191112
Linux dbermudez-XPS-15-9550 5.4.0-42-generic #46~18.04.1-Ubuntu SMP Fri Jul 10 07:21:24 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked unlimited
maxproc  62235 
maxlocks unlimited
maxsignal62235 
maxmessage   819200 
maxnice  40 
maxrtprio50 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   15980220 238792410563004  363232 302929212883024
Swap:   2097148   0 2097148


program versions used
$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $
$Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $

ProgramName: lta_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_annotation2label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_aparc2aseg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_aparc2wmseg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_binarize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.4.0-42-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2020/08/22-19:19:38-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $  User: 

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi there

I uploaded these last week to the file drop and used Bruce's email as it
said it requires a  ".nmr.mgh.harvard.edu" email type.

Please let me know if you received icbm-202 and icbm-205 as tar.gz files.
As I mentioned, I was able to get surfaces for both of these but they
seemed to end at the labeling step.



best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jan 19, 2018 at 10:42 AM, Hoopes, Andrew 
wrote:

> You can send it to either my email (ahoo...@mgh.harvard.edu) or Bruce’s
>
> best,
> Andrew
>
> On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>
>
> thanks Andrew. I had seen that and will give it a go - just wanted to make
> sure that my recipient email would be the FreeSurfer support list.
>
> Trisanna
>
> On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew 
> wrote:
>
>> Hi Trisanna,
>>
>> Okay - if your file is less than 2GiB, I suggest sending your data via
>> the Martinos file drop (directions at the bottom of this page:
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
>>
>> best
>> Andrew
>>
>> On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>>
>> Hi Andrew
>>
>> Thank you for your response. I gave it a go and still no luck, unless I
>> am missing something completely obvious here
>>
>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>> surfer.nmr.mgh.harvard.edu
>> Connected to surfer.nmr.mgh.harvard.edu.
>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>> site
>> 220-shows implicit consent to our Acceptable Use Policy outlined
>> at
>> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>>
>> 220-
>> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-
>> 220-   and nothing happens OR
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-500 Bad EPRT protocol.
>> 220-
>> 220-  try issuing the EPSV command prior to GET or PUT.
>> 220-
>> 220
>> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
>> 331 Please specify the password.
>> Password:
>> 230 Login successful.
>> Remote system type is UNIX.
>> Using binary mode to transfer files.
>> ftp> cd transfer/incoming
>> 250 Directory successfully changed.
>> ftp> quote PASV
>> 227 Entering Passive Mode (132,183,202,158,147,251).
>> ftp> put icbm-205.tar.gz
>> local: icbm-205.tar.gz remote: icbm-205.tar.gz
>> 200 PORT command successful. Consider using PASV.
>> 425 Failed to establish connection.
>>
>>
>>
>>
>>
>> On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew 
>> wrote:
>>
>>> Hi Trisanna,
>>>
>>> Try running 'quote PASV' in ftp before running 'put' - that should
>>> hopefully clear up this issue.
>>>
>>> best,
>>> Andrew
>>>
>>>
>>> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
>>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>>
>>> Sorry, Bruce. ignore my last email. Not sure what happened there.
>>>
>>> I now am trying to upload icbm-205.tar.gz (the subject that failed) but
>>> I get the following and it happens over and over. Any idea what the problem
>>> could be?
>>>
>>> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
>>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
>>> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
>>> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
>>> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
>>> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
>>> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
>>> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
>>> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
>>> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
>>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>>> surfer.nmr.mgh.harvard.edu
>>> Connected to surfer.nmr.mgh.harvard.edu.
>>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>>> site
>>> 220-shows implicit consent to our Acceptable Use Policy outlined
>>> at
>>> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/compute
>>> r/nmr-aup.php
>>> 220-
>>> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
>>> 220-
>>> 220-229 Entering Extended Passive Mode
>>> 220-
>>> 220-   and nothing happens OR
>>> 220-
>>> 220-229 Entering Extended Passive Mode
>>> 220-500 Bad EPRT protocol.
>>> 220-
>>> 220-  try issuing the EPSV command prior to GET or PUT.
>>> 220-
>>> 220
>>> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
>>> 331 Please specify the password.
>>> Password:
>>> 230 Login successful.
>>> Remote system type is UNIX.
>>> Using binary mode to transfer files.
>>> ftp> cd transfer/incoming
>>> 

Re: [Freesurfer] recon-all exited with error

[Hoopes, Andrew]

You can send it to either my email 
(ahoo...@mgh.harvard.edu) or Bruce’s

best,
Andrew

On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much 
>
 wrote:



thanks Andrew. I had seen that and will give it a go - just wanted to make sure 
that my recipient email would be the FreeSurfer support list.

Trisanna

On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew 
> wrote:
Hi Trisanna,

Okay - if your file is less than 2GiB, I suggest sending your data via the 
Martinos file drop (directions at the bottom of this page: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).

best
Andrew

On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much 
>
 wrote:


Hi Andrew

Thank you for your response. I gave it a go and still no luck, unless I am 
missing something completely obvious here

trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp 
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): 
anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> quote PASV
227 Entering Passive Mode (132,183,202,158,147,251).
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.





On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew 
> wrote:
Hi Trisanna,

Try running 'quote PASV' in ftp before running 'put' - that should hopefully 
clear up this issue.

best,
Andrew


On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much 
>
 wrote:

Sorry, Bruce. ignore my last email. Not sure what happened there.

I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get 
the following and it happens over and over. Any idea what the problem could be?

trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] 
surfer.nmr.mgh.harvard.edu
Connected to [X] surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-[X]http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): 
anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much 
>
 wrote:
Thanks Bruce. I have uploaded it but I 

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

thanks Andrew. I had seen that and will give it a go - just wanted to make
sure that my recipient email would be the FreeSurfer support list.

Trisanna

On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew 
wrote:

> Hi Trisanna,
>
> Okay - if your file is less than 2GiB, I suggest sending your data via the
> Martinos file drop (directions at the bottom of this page:
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).
>
> best
> Andrew
>
> On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>
> Hi Andrew
>
> Thank you for your response. I gave it a go and still no luck, unless I am
> missing something completely obvious here
>
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd transfer/incoming
> 250 Directory successfully changed.
> ftp> quote PASV
> 227 Entering Passive Mode (132,183,202,158,147,251).
> ftp> put icbm-205.tar.gz
> local: icbm-205.tar.gz remote: icbm-205.tar.gz
> 200 PORT command successful. Consider using PASV.
> 425 Failed to establish connection.
>
>
>
>
>
> On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew 
> wrote:
>
>> Hi Trisanna,
>>
>> Try running 'quote PASV' in ftp before running 'put' - that should
>> hopefully clear up this issue.
>>
>> best,
>> Andrew
>>
>>
>> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>> Sorry, Bruce. ignore my last email. Not sure what happened there.
>>
>> I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
>> get the following and it happens over and over. Any idea what the problem
>> could be?
>>
>> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
>> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
>> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
>> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
>> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
>> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
>> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
>> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
>> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
>> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
>> surfer.nmr.mgh.harvard.edu
>> Connected to surfer.nmr.mgh.harvard.edu.
>> 220-This is the Martinos Center Anonymous FTP service. Use of this
>> site
>> 220-shows implicit consent to our Acceptable Use Policy outlined
>> at
>> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>>
>> 220-
>> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-
>> 220-   and nothing happens OR
>> 220-
>> 220-229 Entering Extended Passive Mode
>> 220-500 Bad EPRT protocol.
>> 220-
>> 220-  try issuing the EPSV command prior to GET or PUT.
>> 220-
>> 220
>> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
>> 331 Please specify the password.
>> Password:
>> 230 Login successful.
>> Remote system type is UNIX.
>> Using binary mode to transfer files.
>> ftp> cd transfer/incoming
>> 250 Directory successfully changed.
>> ftp> put icbm-205.tar.gz
>> local: icbm-205.tar.gz remote: icbm-205.tar.gz
>> 200 PORT command successful. Consider using PASV.
>> 425 Failed to establish connection.
>>
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <
>> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>>
>>> Thanks Bruce. I have uploaded it but I would like to confirm that you
>>> received the ICBM_305.tar. For some reason I was not able to compress it
>>> any further.
>>>
>>> To clarify, subjects 205 and now subject 202 have both failed after
>>> surface extraction.
>>>
>>> best
>>> Trisanna
>>>
>>> --
>>> Ph.D. Candidate
>>> McGill University
>>> Integrated Program in Neuroscience
>>> Psychology
>>>
>>>
>>> --

Re: [Freesurfer] recon-all exited with error

[Hoopes, Andrew]

Hi Trisanna,

Okay - if your file is less than 2GiB, I suggest sending your data via the 
Martinos file drop (directions at the bottom of this page: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange).

best
Andrew

On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much 
>
 wrote:


Hi Andrew

Thank you for your response. I gave it a go and still no luck, unless I am 
missing something completely obvious here

trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp 
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): 
anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> quote PASV
227 Entering Passive Mode (132,183,202,158,147,251).
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.





On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew 
> wrote:
Hi Trisanna,

Try running 'quote PASV' in ftp before running 'put' - that should hopefully 
clear up this issue.

best,
Andrew


On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much 
>
 wrote:

Sorry, Bruce. ignore my last email. Not sure what happened there.

I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get 
the following and it happens over and over. Any idea what the problem could be?

trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] 
surfer.nmr.mgh.harvard.edu
Connected to [X] surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-[X]http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): 
anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much 
>
 wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received 
the ICBM_305.tar. For some reason I was not able to compress it any further.

To clarify, subjects 205 and now subject 202 have both failed after surface 
extraction.

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl 
> wrote:
you can put it on our 

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi Andrew

Thank you for your response. I gave it a go and still no luck, unless I am
missing something completely obvious here

trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> quote PASV
227 Entering Passive Mode (132,183,202,158,147,251).
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.





On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew 
wrote:

> Hi Trisanna,
>
> Try running 'quote PASV' in ftp before running 'put' - that should
> hopefully clear up this issue.
>
> best,
> Andrew
>
>
> On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Sorry, Bruce. ignore my last email. Not sure what happened there.
>
> I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
> get the following and it happens over and over. Any idea what the problem
> could be?
>
> trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
> fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
> icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
> icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
> icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
> icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
> icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
> icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
> icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
> trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd transfer/incoming
> 250 Directory successfully changed.
> ftp> put icbm-205.tar.gz
> local: icbm-205.tar.gz remote: icbm-205.tar.gz
> 200 PORT command successful. Consider using PASV.
> 425 Failed to establish connection.
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <
> trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
>> Thanks Bruce. I have uploaded it but I would like to confirm that you
>> received the ICBM_305.tar. For some reason I was not able to compress it
>> any further.
>>
>> To clarify, subjects 205 and now subject 202 have both failed after
>> surface extraction.
>>
>> best
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl > > wrote:
>>
>>> you can put it on our ftp site:
>>>
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>>> On Tue, 16 Jan
>>> 2018, Trisanna Sprung-Much
>>> wrote:
>>>
>>> > Hi Bruce
>>> > Thanks for the speedy reply. Should I attach it here or is there a
>>> place I can upload it to?
>>> >
>>> > best
>>> > Trisanna
>>> >
>>> > --
>>> > Ph.D. CandidateMcGill University
>>> > Integrated Program in Neuroscience
>>> > Psychology
>>> >
>>> >
>>> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> >   hmmm, I've never seen 

Re: [Freesurfer] recon-all exited with error

[Hoopes, Andrew]

Hi Trisanna,

Try running 'quote PASV' in ftp before running 'put' - that should hopefully 
clear up this issue.

best,
Andrew


On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much 
>
 wrote:

Sorry, Bruce. ignore my last email. Not sure what happened there.

I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get 
the following and it happens over and over. Any idea what the problem could be?

trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] 
surfer.nmr.mgh.harvard.edu
Connected to [X] surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-[X]http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): 
anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much 
>
 wrote:
Thanks Bruce. I have uploaded it but I would like to confirm that you received 
the ICBM_305.tar. For some reason I was not able to compress it any further.

To clarify, subjects 205 and now subject 202 have both failed after surface 
extraction.

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl 
> wrote:
you can put it on our ftp site:

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Tue, 16 Jan
2018, Trisanna Sprung-Much
wrote:

> Hi Bruce
> Thanks for the speedy reply. Should I attach it here or is there a place I 
> can upload it to?
>
> best
> Trisanna
>
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl 
> > wrote:
>   hmmm, I've never seen label2label core dump before. Can you tar, gzip 
> and
>   upload the entire subject dir?
>   On Tue, 16 Jan 2018, Trisanna Sprung-Much
>   wrote:
>
>   > Hi there
>   >
>   > I ran Freesurfer 6.0 on a subject last night and it took about 12 
> hours (seemed to get
>   to the very end) and then exited with
>   > errors. I can open my surfaces so I think it ended roughly with the 
> atlas labelling. I
>   attach the recon-all log file here.
>   >
>   > best wishes
>   >
>   > Trisanna
>   > --
>   > Ph.D. CandidateMcGill University
>   > Integrated Program in Neuroscience
>   > Psychology
>   >
>   >
>   >
>   >
>   ___
>   Freesurfer mailing list
>   Freesurfer@nmr.mgh.harvard.edu
>   [X] [X] 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
>   [X] [X] http://www.partners.org/complianceline . If the e-mail was sent 
> to you in error
>   but does not contain patient information, please 

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Sorry, Bruce. ignore my last email. Not sure what happened there.

I now am trying to upload icbm-205.tar.gz (the subject that failed) but I
get the following and it happens over and over. Any idea what the problem
could be?

trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls
fsaverage  icbm-109  icbm-118  icbm-127  icbm-142  icbm-202
icbm-102   icbm-110  icbm-119  icbm-131  icbm-143  icbm-202.tar.gz
icbm-103   icbm-111  icbm-120  icbm-133  icbm-144  icbm-203
icbm-104   icbm-112  icbm-121  icbm-135  icbm-146  icbm-204
icbm-105   icbm-113  icbm-122  icbm-137  icbm-150  icbm-205
icbm-106   icbm-114  icbm-123  icbm-139  icbm-158  icbm-205.tar.gz
icbm-107   icbm-115  icbm-125  icbm-140  icbm-200  icbm-206
icbm-108   icbm-117  icbm-126  icbm-141  icbm-201
trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put icbm-205.tar.gz
local: icbm-205.tar.gz remote: icbm-205.tar.gz
200 PORT command successful. Consider using PASV.
425 Failed to establish connection.


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:

> Thanks Bruce. I have uploaded it but I would like to confirm that you
> received the ICBM_305.tar. For some reason I was not able to compress it
> any further.
>
> To clarify, subjects 205 and now subject 202 have both failed after
> surface extraction.
>
> best
> Trisanna
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl 
> wrote:
>
>> you can put it on our ftp site:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
>> On Tue, 16 Jan
>> 2018, Trisanna Sprung-Much
>> wrote:
>>
>> > Hi Bruce
>> > Thanks for the speedy reply. Should I attach it here or is there a
>> place I can upload it to?
>> >
>> > best
>> > Trisanna
>> >
>> > --
>> > Ph.D. CandidateMcGill University
>> > Integrated Program in Neuroscience
>> > Psychology
>> >
>> >
>> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   hmmm, I've never seen label2label core dump before. Can you tar,
>> gzip and
>> >   upload the entire subject dir?
>> >   On Tue, 16 Jan 2018, Trisanna Sprung-Much
>> >   wrote:
>> >
>> >   > Hi there
>> >   >
>> >   > I ran Freesurfer 6.0 on a subject last night and it took about
>> 12 hours (seemed to get
>> >   to the very end) and then exited with
>> >   > errors. I can open my surfaces so I think it ended roughly with
>> the atlas labelling. I
>> >   attach the recon-all log file here.
>> >   >
>> >   > best wishes
>> >   >
>> >   > Trisanna
>> >   > --
>> >   > Ph.D. CandidateMcGill University
>> >   > Integrated Program in Neuroscience
>> >   > Psychology
>> >   >
>> >   >
>> >   >
>> >   >
>> >   ___
>> >   Freesurfer mailing list
>> >   Freesurfer@nmr.mgh.harvard.edu
>> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >   The information in this e-mail is intended only for the person to
>> whom it is
>> >   addressed. If you believe this e-mail was sent to you in error
>> and the e-mail
>> >   contains patient information, please contact the Partners
>> Compliance HelpLine at
>> >   http://www.partners.org/complianceline . If the e-mail was sent
>> to you in error
>> >   but does not contain patient information, please contact the
>> sender and properly
>> >   dispose of the e-mail.
>> >
>> >
>> >
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
___
Freesurfer mailing list

Re: [Freesurfer] recon-all exited with error

[Bruce Fischl]

Hi Trisanna

there are a bunch of files, but they all look like they are empty:

r--r--r-- 1 ftpftp   0 Jan 17 14:24 ICBM_305.tar
-r--r--r-- 1 ftpftp   0 Jan 17 14:41 ICBM_305.tar.gz
-r--r--r-- 1 ftpftp   0 Jan 17 15:12 icbm-205.tar.gz


cheers
Bruce
On Wed, 
17 Jan 2018, Trisanna Sprung-Much wrote:



Thanks Bruce. I have uploaded it but I would like to confirm that you received 
the ICBM_305.tar. For
some reason I was not able to compress it any further.

To clarify, subjects 205 and now subject 202 have both failed after surface 
extraction.

best
Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl  
wrote:
  you can put it on our ftp site:

  https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
  On Tue, 16 Jan
  2018, Trisanna Sprung-Much
  wrote:

  > Hi Bruce
  > Thanks for the speedy reply. Should I attach it here or is there a 
place I can upload
  it to?
  >
  > best
  > Trisanna
  >
  > --
  > Ph.D. CandidateMcGill University
  > Integrated Program in Neuroscience
  > Psychology
  >
  >
  > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl 
 wrote:
  >       hmmm, I've never seen label2label core dump before. Can you tar, 
gzip and
  >       upload the entire subject dir?
  >       On Tue, 16 Jan 2018, Trisanna Sprung-Much
  >       wrote:
  >
  >       > Hi there
  >       >
  >       > I ran Freesurfer 6.0 on a subject last night and it took about 
12 hours
  (seemed to get
  >       to the very end) and then exited with
  >       > errors. I can open my surfaces so I think it ended roughly with 
the atlas
  labelling. I
  >       attach the recon-all log file here.
  >       >
  >       > best wishes
  >       >
  >       > Trisanna
  >       > --
  >       > Ph.D. CandidateMcGill University
  >       > Integrated Program in Neuroscience
  >       > Psychology
  >       >
  >       >
  >       >
  >       >
  >       ___
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >       The information in this e-mail is intended only for the person to 
whom it is
  >       addressed. If you believe this e-mail was sent to you in error 
and the e-mail
  >       contains patient information, please contact the Partners 
Compliance HelpLine at
  >       http://www.partners.org/complianceline . If the e-mail was sent 
to you in error
  >       but does not contain patient information, please contact the 
sender and properly
  >       dispose of the e-mail.
  >
  >
  >
  >
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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


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

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Thanks Bruce. I have uploaded it but I would like to confirm that you
received the ICBM_305.tar. For some reason I was not able to compress it
any further.

To clarify, subjects 205 and now subject 202 have both failed after surface
extraction.

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl 
wrote:

> you can put it on our ftp site:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
> On Tue, 16 Jan
> 2018, Trisanna Sprung-Much
> wrote:
>
> > Hi Bruce
> > Thanks for the speedy reply. Should I attach it here or is there a place
> I can upload it to?
> >
> > best
> > Trisanna
> >
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   hmmm, I've never seen label2label core dump before. Can you tar,
> gzip and
> >   upload the entire subject dir?
> >   On Tue, 16 Jan 2018, Trisanna Sprung-Much
> >   wrote:
> >
> >   > Hi there
> >   >
> >   > I ran Freesurfer 6.0 on a subject last night and it took about
> 12 hours (seemed to get
> >   to the very end) and then exited with
> >   > errors. I can open my surfaces so I think it ended roughly with
> the atlas labelling. I
> >   attach the recon-all log file here.
> >   >
> >   > best wishes
> >   >
> >   > Trisanna
> >   > --
> >   > Ph.D. CandidateMcGill University
> >   > Integrated Program in Neuroscience
> >   > Psychology
> >   >
> >   >
> >   >
> >   >
> >   ___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >   The information in this e-mail is intended only for the person to
> whom it is
> >   addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> >   contains patient information, please contact the Partners
> Compliance HelpLine at
> >   http://www.partners.org/complianceline . If the e-mail was sent
> to you in error
> >   but does not contain patient information, please contact the
> sender and properly
> >   dispose of the e-mail.
> >
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] recon-all exited with error

[Bruce Fischl]

you can put it on our ftp site:

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Tue, 16 Jan 
2018, Trisanna Sprung-Much 
wrote:

> Hi Bruce
> Thanks for the speedy reply. Should I attach it here or is there a place I 
> can upload it to?
> 
> best
> Trisanna
> 
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl  
> wrote:
>   hmmm, I've never seen label2label core dump before. Can you tar, gzip 
> and
>   upload the entire subject dir?
>   On Tue, 16 Jan 2018, Trisanna Sprung-Much
>   wrote:
>
>   > Hi there
>   >
>   > I ran Freesurfer 6.0 on a subject last night and it took about 12 
> hours (seemed to get
>   to the very end) and then exited with
>   > errors. I can open my surfaces so I think it ended roughly with the 
> atlas labelling. I
>   attach the recon-all log file here.
>   >
>   > best wishes
>   >
>   > Trisanna
>   > --
>   > Ph.D. CandidateMcGill University
>   > Integrated Program in Neuroscience
>   > Psychology
>   >
>   >
>   >
>   >
>   ___
>   Freesurfer mailing list
>   Freesurfer@nmr.mgh.harvard.edu
>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>   The information in this e-mail is intended only for the person to whom 
> it is
>   addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
>   contains patient information, please contact the Partners Compliance 
> HelpLine at
>   http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
>   but does not contain patient information, please contact the sender and 
> properly
>   dispose of the e-mail.
> 
> 
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi Bruce

Thanks for the speedy reply. Should I attach it here or is there a place I
can upload it to?

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl 
wrote:

> hmmm, I've never seen label2label core dump before. Can you tar, gzip and
> upload the entire subject dir?
> On Tue, 16 Jan 2018, Trisanna Sprung-Much
> wrote:
>
> > Hi there
> >
> > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours
> (seemed to get to the very end) and then exited with
> > errors. I can open my surfaces so I think it ended roughly with the
> atlas labelling. I attach the recon-all log file here.
> >
> > best wishes
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] recon-all exited with error

[Bruce Fischl]

hmmm, I've never seen label2label core dump before. Can you tar, gzip and 
upload the entire subject dir?
On Tue, 16 Jan 2018, Trisanna Sprung-Much 
wrote:

> Hi there
> 
> I ran Freesurfer 6.0 on a subject last night and it took about 12 hours 
> (seemed to get to the very end) and then exited with
> errors. I can open my surfaces so I think it ended roughly with the atlas 
> labelling. I attach the recon-all log file here.
> 
> best wishes
> 
> Trisanna
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] recon-all exited with error.

[miracle ozzoude]

Hello Z K,
Thank you. I will do it later and update you.
Best,
Paul

On Mon, Mar 6, 2017 at 9:07 AM, Z K  wrote:

> Hello Paul,
>
> I've been trying to replicate it the issue on my Mac without any success.
> But I do have what might be a potential solution ide like you to try. Could
> you please
> source freesurfer, then run the following command.
>
>  $> sudo -E fs_update
>
> (This will update a freesurfer file on your machine). Then retry the
> subject with the parallel flag. Please let me know how it goes. Thanks.
>
> -Zeke
>
> On Mar 6, 2017, at 8:56 AM, miracle ozzoude  wrote:
>
> Hello Z K,
> Were you able to fix the bug?
> Best,
> Paul
>
> On Fri, Mar 3, 2017 at 12:14 PM, Z K  wrote:
>
>> Im looking into this now, but I think their might be a bug when using
>> the -parallel flag on Mac platforms. I should have a fix shortly. I will
>> let you know.
>>
>> On 03/03/2017 12:10 PM, miracle ozzoude wrote:
>> > Thanks Antonin. I also have different error when running another
>> > subject. Recon fails in the smooth stage of recon-all (please see the
>> > attached screenshot). How can i fix this?
>> > Best,
>> > Paul
>> >
>> >
>> > On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch > > > wrote:
>> >
>> > Dear Paul,
>> >
>> > yes, this is the modification of FREESURFER_HOME you need to do
>> > (using setenv command if you are using tcsh).
>> >
>> > Regards,
>> >
>> > Antonin
>> >
>> >
>> > Hey Antonin,
>> > Thank you. hence, the right path should be "setenv FREESURFER_HOME
>> > /opt/freesurfer-6.0.0/freesurfer "
>> > Best,
>> > Paul.
>> >
>> > On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch > > wrote:
>> >
>> > > Dear Paul,
>> > >
>> > > the slash problem prevents to properly create symbolic link to
>> fsaverage in
>> > > your SUBJECTS_DIR.
>> > >
>> > > Then, the mri_label2label could not find the fsaverage label file
>> since
>> > > symbolic link for fsaverage does not exist, hence produces the
>> error.log you
>> > > are attaching.
>> > >
>> > > Regards,
>> > >
>> > > Antonin
>> > >
>> > >
>> > > Thanks Antonin. Also, I got this error.log file in my label
>> folder. Do you
>> > > think it is due to the slash problem?
>> > > Best,
>> > > Paul
>> > >
>> > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch > > wrote:
>> > >
>> > > > Dear Paul,
>> > > >
>> > > > I suppose the clue is following messages from your
>> recon-all.log file:
>> > > >
>> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
>> > > >
>> > > > and
>> > > >
>> > > >  cd /net/synapse/nt/mozzoude/proce
>> ssing/freesurfer/176_003_120326; ln -s
>> > > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
>> > > >
>> > > > ln: failed to create symbolic link './fsaverage': File exists
>> > > >
>> > > > The problem is that your FREESURFER_HOME contains slash in the
>> end. Remove
>> > > > it
>> > > > and rerun relevant part of recon-all. It should work then.
>> > > >
>> > > > Antonin
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > Hello Freesurfer,
>> > > > I was running recon-all in steps (recon-all -autorecon1,
>> recon-all
>> > > > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial
>> autorecon3). However,
>> > > > it exited with error during the BA_exvivo labels part of
>> autorecon3 (please
>> > > > see attached recon-all.log file). Please, how can I fix it?
>> Thanks
>> > > > Best,
>> > > > Paul
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu > vard.edu>
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > 
>> >
>> >
>> > The information in this e-mail is intended only for the person to
>> > whom it is
>> > addressed. If you believe this e-mail was sent to you in error and
>> > the e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline
>> >  . If the e-mail was sent
>> to
>> > you in error
>> > but does not contain patient information, please contact the sender
>> > and properly
>> > dispose of the e-mail.
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 

Re: [Freesurfer] recon-all exited with error.

[Z K]

Hello Paul,

I've been trying to replicate it the issue on my Mac without any success. But I 
do have what might be a potential solution ide like you to try. Could you please
source freesurfer, then run the following command.

 $> sudo -E fs_update

(This will update a freesurfer file on your machine). Then retry the subject 
with the parallel flag. Please let me know how it goes. Thanks.

-Zeke

> On Mar 6, 2017, at 8:56 AM, miracle ozzoude  wrote:
> 
> Hello Z K, 
> Were you able to fix the bug?
> Best, 
> Paul
> 
>> On Fri, Mar 3, 2017 at 12:14 PM, Z K  wrote:
>> Im looking into this now, but I think their might be a bug when using
>> the -parallel flag on Mac platforms. I should have a fix shortly. I will
>> let you know.
>> 
>> On 03/03/2017 12:10 PM, miracle ozzoude wrote:
>> > Thanks Antonin. I also have different error when running another
>> > subject. Recon fails in the smooth stage of recon-all (please see the
>> > attached screenshot). How can i fix this?
>> > Best,
>> > Paul
>> >
>> >
>> > On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch > > > wrote:
>> >
>> > Dear Paul,
>> >
>> > yes, this is the modification of FREESURFER_HOME you need to do
>> > (using setenv command if you are using tcsh).
>> >
>> > Regards,
>> >
>> > Antonin
>> >
>> >
>> > Hey Antonin,
>> > Thank you. hence, the right path should be "setenv FREESURFER_HOME
>> > /opt/freesurfer-6.0.0/freesurfer "
>> > Best,
>> > Paul.
>> >
>> > On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch > > > wrote:
>> >
>> > > Dear Paul,
>> > >
>> > > the slash problem prevents to properly create symbolic link to 
>> > fsaverage in
>> > > your SUBJECTS_DIR.
>> > >
>> > > Then, the mri_label2label could not find the fsaverage label file 
>> > since
>> > > symbolic link for fsaverage does not exist, hence produces the 
>> > error.log you
>> > > are attaching.
>> > >
>> > > Regards,
>> > >
>> > > Antonin
>> > >
>> > >
>> > > Thanks Antonin. Also, I got this error.log file in my label folder. 
>> > Do you
>> > > think it is due to the slash problem?
>> > > Best,
>> > > Paul
>> > >
>> > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch > > > wrote:
>> > >
>> > > > Dear Paul,
>> > > >
>> > > > I suppose the clue is following messages from your recon-all.log 
>> > file:
>> > > >
>> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
>> > > >
>> > > > and
>> > > >
>> > > >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; 
>> > ln -s
>> > > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
>> > > >
>> > > > ln: failed to create symbolic link './fsaverage': File exists
>> > > >
>> > > > The problem is that your FREESURFER_HOME contains slash in the 
>> > end. Remove
>> > > > it
>> > > > and rerun relevant part of recon-all. It should work then.
>> > > >
>> > > > Antonin
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > Hello Freesurfer,
>> > > > I was running recon-all in steps (recon-all -autorecon1, recon-all
>> > > > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). 
>> > However,
>> > > > it exited with error during the BA_exvivo labels part of 
>> > autorecon3 (please
>> > > > see attached recon-all.log file). Please, how can I fix it? Thanks
>> > > > Best,
>> > > > Paul
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu 
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> > 
>> >
>> >
>> > The information in this e-mail is intended only for the person to
>> > whom it is
>> > addressed. If you believe this e-mail was sent to you in error and
>> > the e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline
>> >  . If the e-mail was sent to
>> > you in error
>> > but does not contain patient information, please contact the sender
>> > and properly
>> > dispose of the e-mail.
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
> Freesurfer mailing list
> 

Re: [Freesurfer] recon-all exited with error.

[miracle ozzoude]

Hello Z K,
Were you able to fix the bug?
Best,
Paul

On Fri, Mar 3, 2017 at 12:14 PM, Z K  wrote:

> Im looking into this now, but I think their might be a bug when using
> the -parallel flag on Mac platforms. I should have a fix shortly. I will
> let you know.
>
> On 03/03/2017 12:10 PM, miracle ozzoude wrote:
> > Thanks Antonin. I also have different error when running another
> > subject. Recon fails in the smooth stage of recon-all (please see the
> > attached screenshot). How can i fix this?
> > Best,
> > Paul
> >
> >
> > On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch  > > wrote:
> >
> > Dear Paul,
> >
> > yes, this is the modification of FREESURFER_HOME you need to do
> > (using setenv command if you are using tcsh).
> >
> > Regards,
> >
> > Antonin
> >
> >
> > Hey Antonin,
> > Thank you. hence, the right path should be "setenv FREESURFER_HOME
> > /opt/freesurfer-6.0.0/freesurfer "
> > Best,
> > Paul.
> >
> > On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch > wrote:
> >
> > > Dear Paul,
> > >
> > > the slash problem prevents to properly create symbolic link to
> fsaverage in
> > > your SUBJECTS_DIR.
> > >
> > > Then, the mri_label2label could not find the fsaverage label file
> since
> > > symbolic link for fsaverage does not exist, hence produces the
> error.log you
> > > are attaching.
> > >
> > > Regards,
> > >
> > > Antonin
> > >
> > >
> > > Thanks Antonin. Also, I got this error.log file in my label
> folder. Do you
> > > think it is due to the slash problem?
> > > Best,
> > > Paul
> > >
> > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  > wrote:
> > >
> > > > Dear Paul,
> > > >
> > > > I suppose the clue is following messages from your recon-all.log
> file:
> > > >
> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
> > > >
> > > > and
> > > >
> > > >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326;
> ln -s
> > > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
> > > >
> > > > ln: failed to create symbolic link './fsaverage': File exists
> > > >
> > > > The problem is that your FREESURFER_HOME contains slash in the
> end. Remove
> > > > it
> > > > and rerun relevant part of recon-all. It should work then.
> > > >
> > > > Antonin
> > > >
> > > >
> > > >
> > > >
> > > > Hello Freesurfer,
> > > > I was running recon-all in steps (recon-all -autorecon1,
> recon-all
> > > > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial
> autorecon3). However,
> > > > it exited with error during the BA_exvivo labels part of
> autorecon3 (please
> > > > see attached recon-all.log file). Please, how can I fix it?
> Thanks
> > > > Best,
> > > > Paul
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline
> >  . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the sender
> > and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] recon-all exited with error.

[miracle ozzoude]

Thanks. Z K
Best,
Paul

On Fri, Mar 3, 2017 at 12:14 PM, Z K  wrote:

> Im looking into this now, but I think their might be a bug when using
> the -parallel flag on Mac platforms. I should have a fix shortly. I will
> let you know.
>
> On 03/03/2017 12:10 PM, miracle ozzoude wrote:
> > Thanks Antonin. I also have different error when running another
> > subject. Recon fails in the smooth stage of recon-all (please see the
> > attached screenshot). How can i fix this?
> > Best,
> > Paul
> >
> >
> > On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch  > > wrote:
> >
> > Dear Paul,
> >
> > yes, this is the modification of FREESURFER_HOME you need to do
> > (using setenv command if you are using tcsh).
> >
> > Regards,
> >
> > Antonin
> >
> >
> > Hey Antonin,
> > Thank you. hence, the right path should be "setenv FREESURFER_HOME
> > /opt/freesurfer-6.0.0/freesurfer "
> > Best,
> > Paul.
> >
> > On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch > wrote:
> >
> > > Dear Paul,
> > >
> > > the slash problem prevents to properly create symbolic link to
> fsaverage in
> > > your SUBJECTS_DIR.
> > >
> > > Then, the mri_label2label could not find the fsaverage label file
> since
> > > symbolic link for fsaverage does not exist, hence produces the
> error.log you
> > > are attaching.
> > >
> > > Regards,
> > >
> > > Antonin
> > >
> > >
> > > Thanks Antonin. Also, I got this error.log file in my label
> folder. Do you
> > > think it is due to the slash problem?
> > > Best,
> > > Paul
> > >
> > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  > wrote:
> > >
> > > > Dear Paul,
> > > >
> > > > I suppose the clue is following messages from your recon-all.log
> file:
> > > >
> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
> > > >
> > > > and
> > > >
> > > >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326;
> ln -s
> > > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
> > > >
> > > > ln: failed to create symbolic link './fsaverage': File exists
> > > >
> > > > The problem is that your FREESURFER_HOME contains slash in the
> end. Remove
> > > > it
> > > > and rerun relevant part of recon-all. It should work then.
> > > >
> > > > Antonin
> > > >
> > > >
> > > >
> > > >
> > > > Hello Freesurfer,
> > > > I was running recon-all in steps (recon-all -autorecon1,
> recon-all
> > > > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial
> autorecon3). However,
> > > > it exited with error during the BA_exvivo labels part of
> autorecon3 (please
> > > > see attached recon-all.log file). Please, how can I fix it?
> Thanks
> > > > Best,
> > > > Paul
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline
> >  . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the sender
> > and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] recon-all exited with error.

[Z K]

Im looking into this now, but I think their might be a bug when using 
the -parallel flag on Mac platforms. I should have a fix shortly. I will 
let you know.

On 03/03/2017 12:10 PM, miracle ozzoude wrote:
> Thanks Antonin. I also have different error when running another
> subject. Recon fails in the smooth stage of recon-all (please see the
> attached screenshot). How can i fix this?
> Best,
> Paul
>
>
> On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch  > wrote:
>
> Dear Paul,
>
> yes, this is the modification of FREESURFER_HOME you need to do
> (using setenv command if you are using tcsh).
>
> Regards,
>
> Antonin
>
>
> Hey Antonin,
> Thank you. hence, the right path should be "setenv FREESURFER_HOME
> /opt/freesurfer-6.0.0/freesurfer "
> Best,
> Paul.
>
> On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch  > wrote:
>
> > Dear Paul,
> >
> > the slash problem prevents to properly create symbolic link to 
> fsaverage in
> > your SUBJECTS_DIR.
> >
> > Then, the mri_label2label could not find the fsaverage label file since
> > symbolic link for fsaverage does not exist, hence produces the 
> error.log you
> > are attaching.
> >
> > Regards,
> >
> > Antonin
> >
> >
> > Thanks Antonin. Also, I got this error.log file in my label folder. Do 
> you
> > think it is due to the slash problem?
> > Best,
> > Paul
> >
> > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  > wrote:
> >
> > > Dear Paul,
> > >
> > > I suppose the clue is following messages from your recon-all.log file:
> > >
> > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
> > >
> > > and
> > >
> > >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln 
> -s
> > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
> > >
> > > ln: failed to create symbolic link './fsaverage': File exists
> > >
> > > The problem is that your FREESURFER_HOME contains slash in the end. 
> Remove
> > > it
> > > and rerun relevant part of recon-all. It should work then.
> > >
> > > Antonin
> > >
> > >
> > >
> > >
> > > Hello Freesurfer,
> > > I was running recon-all in steps (recon-all -autorecon1, recon-all
> > > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). 
> However,
> > > it exited with error during the BA_exvivo labels part of autorecon3 
> (please
> > > see attached recon-all.log file). Please, how can I fix it? Thanks
> > > Best,
> > > Paul
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline
>  . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all exited with error.

[Antonin Skoch]

Dear Paul,

yes, this is the modification of FREESURFER_HOME you need to do (using setenv 
command if you are using tcsh).

Regards, 

Antonin


Hey Antonin,
Thank you. hence, the right path should be "setenv FREESURFER_HOME
/opt/freesurfer-6.0.0/freesurfer "
Best,
Paul.
On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> the slash problem prevents to properly create symbolic link to fsaverage in 
> your SUBJECTS_DIR.
>
> Then, the mri_label2label could not find the fsaverage label file since 
> symbolic link for fsaverage does not exist, hence produces the error.log you 
> are attaching.
>
> Regards,
>
> Antonin
>
>
> Thanks Antonin. Also, I got this error.log file in my label folder. Do you
> think it is due to the slash problem?
> Best,
> Paul
>
> On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  wrote:
>
> > Dear Paul,
> >
> > I suppose the clue is following messages from your recon-all.log file:
> >
> > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
> >
> > and
> >
> >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s
> > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
> >
> > ln: failed to create symbolic link './fsaverage': File exists
> >
> > The problem is that your FREESURFER_HOME contains slash in the end. Remove 
> > it
> > and rerun relevant part of recon-all. It should work then.
> >
> > Antonin
> >
> >
> >
> >
> > Hello Freesurfer,
> > I was running recon-all in steps (recon-all -autorecon1, recon-all
> > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). However,
> > it exited with error during the BA_exvivo labels part of autorecon3 (please
> > see attached recon-all.log file). Please, how can I fix it? Thanks
> > Best,
> > Paul
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] recon-all exited with error.

[miracle ozzoude]

Hey Antonin,
Thank you. hence, the right path should be "setenv FREESURFER_HOME
/opt/freesurfer-6.0.0/freesurfer "
Best,
Paul.


On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> the slash problem prevents to properly create symbolic link to fsaverage in 
> your SUBJECTS_DIR.
>
> Then, the mri_label2label could not find the fsaverage label file since 
> symbolic link for fsaverage does not exist, hence produces the error.log you 
> are attaching.
>
> Regards,
>
> Antonin
>
>
> Thanks Antonin. Also, I got this error.log file in my label folder. Do you
> think it is due to the slash problem?
> Best,
> Paul
>
> On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  wrote:
>
> > Dear Paul,
> >
> > I suppose the clue is following messages from your recon-all.log file:
> >
> > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
> >
> > and
> >
> >  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s
> > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
> >
> > ln: failed to create symbolic link './fsaverage': File exists
> >
> > The problem is that your FREESURFER_HOME contains slash in the end. Remove 
> > it
> > and rerun relevant part of recon-all. It should work then.
> >
> > Antonin
> >
> >
> >
> >
> > Hello Freesurfer,
> > I was running recon-all in steps (recon-all -autorecon1, recon-all
> > -autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). However,
> > it exited with error during the BA_exvivo labels part of autorecon3 (please
> > see attached recon-all.log file). Please, how can I fix it? Thanks
> > Best,
> > Paul
>
>
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Re: [Freesurfer] recon-all exited with error.

[Antonin Skoch]

Dear Paul,

the slash problem prevents to properly create symbolic link to fsaverage in 
your SUBJECTS_DIR.

Then, the mri_label2label could not find the fsaverage label file since 
symbolic link for fsaverage does not exist, hence produces the error.log you 
are attaching.

Regards,

Antonin


Thanks Antonin. Also, I got this error.log file in my label folder. Do you
think it is due to the slash problem?
Best,
PaulOn Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I suppose the clue is following messages from your recon-all.log file:
>
> FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
>
> and
>
>  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s 
> /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
>
> ln: failed to create symbolic link './fsaverage': File exists
>
> The problem is that your FREESURFER_HOME contains slash in the end. Remove it 
> and rerun relevant part of recon-all. It should work then.
>
> Antonin
>
>
>
>
> Hello Freesurfer,
> I was running recon-all in steps (recon-all -autorecon1, recon-all
> -autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). However,
> it exited with error during the BA_exvivo labels part of autorecon3 (please
> see attached recon-all.log file). Please, how can I fix it? Thanks
> Best,
> Paul___
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Re: [Freesurfer] recon-all exited with error.

[miracle ozzoude]

Thanks Antonin. Also, I got this error.log file in my label folder. Do you
think it is due to the slash problem?
Best,
Paul

On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I suppose the clue is following messages from your recon-all.log file:
>
> FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
>
> and
>
>  cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s 
> /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
>
> ln: failed to create symbolic link './fsaverage': File exists
>
> The problem is that your FREESURFER_HOME contains slash in the end. Remove it 
> and rerun relevant part of recon-all. It should work then.
>
> Antonin
>
>
>
>
> Hello Freesurfer,
> I was running recon-all in steps (recon-all -autorecon1, recon-all
> -autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). However,
> it exited with error during the BA_exvivo labels part of autorecon3 (please
> see attached recon-all.log file). Please, how can I fix it? Thanks
> Best,
> Paul
>
>
> ___
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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.
>
>


error.log
Description: Binary data
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Re: [Freesurfer] recon-all exited with error.

[Antonin Skoch]

Dear Paul,

I suppose the clue is following messages from your recon-all.log file:

FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/

and
 cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s 
/opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - 

ln: failed to create symbolic link './fsaverage': File exists

The problem is that your FREESURFER_HOME contains slash in the end. Remove it 
and rerun relevant part of recon-all. It should work then.

Antonin



Hello Freesurfer,
I was running recon-all in steps (recon-all -autorecon1, recon-all
-autorecon2, and recon-all - -T2 /T2 volume  -T2pial autorecon3). However,
it exited with error during the BA_exvivo labels part of autorecon3 (please
see attached recon-all.log file). Please, how can I fix it? Thanks
Best,
Paul___
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Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

[Vaz pandolfo, Renata]

Okay, I changed some other things and now the recon-all is running.
I will see how it looks tomorrow.

I used:
recon-all -all \
> -i
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
-s new_trial_20110815 \
> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
> -T2
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
\
> -T2pial -hippocampal-subfields-T1

Thanks!


On Thu, Jul 7, 2016 at 2:15 PM, Vaz pandolfo, Renata <r...@njit.edu> wrote:

> Thank you!
>
> But now the error is:
>
> ERROR: cannot find
> o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
> Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016
>
> Maybe I have to put the whole path?
>
> On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. <krieg...@upmc.edu>
> wrote:
>
>> Hi Renata,
>>
>>
>>
>> Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/
>>
>>
>>
>> HTH - Don
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
>> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo,
>> Renata
>> *Sent:* Thursday, July 07, 2016 8:05 AM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* [Freesurfer] recon-all exited with error: reading
>> lh.BA1_exvivo.label
>>
>>
>>
>> Dear FreeSurfer developers,
>>
>> I am running recon-all on a healthy subject and I am also trying to get
>> the hippocampal subfields segmentation.
>> On the mri directory there is no hippocampus output, and the recon-all
>> exited with errors.
>> From my understanding, the error is with the lh.BA1_exvivo.label:
>>
>> SUBJECTS_DIR
>> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
>> FREESURFER_HOME /usr/local/freesurfer
>> Loading source label.
>> Invalid argument
>> ERROR reading
>> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label
>>
>> The command I used was:
>> recon-all -all \
>> -i
>> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
>> -s 20110815/ \
>> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
>> -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
>> -T2pial -hippocampal-subfields-T1
>>
>>
>> When trying to solve the problem, I noticed that I could have run a
>> separate command for the hippocampal subfields and I ran this one:
>>
>>
>> recon-all \
>> -s 20110815/ \
>> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
>> -hippocampal-subfields-T1T2
>> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
>> 20110815_T2
>>
>> Since the previous data had errors, I didn't really expect this to work,
>> but I tried it anyways.
>>
>> It exited "without errors", but on the log there was the following error
>> twice:
>>
>> Error:Cannot find CTF archive
>> /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
>>
>> Extra info:
>>
>> Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
>>
>> uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37
>> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> logs: recon-all and hippocampal-subfields-T1T2 attached
>>
>> If anyone has had the same problem, could you please tell me how to solve
>> it?
>> And if I am doing something wrong, please tell me the correct way so I
>> can continue with the analysis.
>>
>>
>>
>> Thank you!
>>
>> Renata
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

[Vaz pandolfo, Renata]

Thank you!

But now the error is:

ERROR: cannot find
o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016

Maybe I have to put the whole path?

On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. <krieg...@upmc.edu>
wrote:

> Hi Renata,
>
>
>
> Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/
>
>
>
> HTH - Don
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo,
> Renata
> *Sent:* Thursday, July 07, 2016 8:05 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] recon-all exited with error: reading
> lh.BA1_exvivo.label
>
>
>
> Dear FreeSurfer developers,
>
> I am running recon-all on a healthy subject and I am also trying to get
> the hippocampal subfields segmentation.
> On the mri directory there is no hippocampus output, and the recon-all
> exited with errors.
> From my understanding, the error is with the lh.BA1_exvivo.label:
>
> SUBJECTS_DIR
> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
> FREESURFER_HOME /usr/local/freesurfer
> Loading source label.
> Invalid argument
> ERROR reading
> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label
>
> The command I used was:
> recon-all -all \
> -i
> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
> -s 20110815/ \
> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
> -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
> -T2pial -hippocampal-subfields-T1
>
>
> When trying to solve the problem, I noticed that I could have run a
> separate command for the hippocampal subfields and I ran this one:
>
>
> recon-all \
> -s 20110815/ \
> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
> -hippocampal-subfields-T1T2
> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
> 20110815_T2
>
> Since the previous data had errors, I didn't really expect this to work,
> but I tried it anyways.
>
> It exited "without errors", but on the log there was the following error
> twice:
>
> Error:Cannot find CTF archive
> /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
>
> Extra info:
>
> Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
>
> uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> logs: recon-all and hippocampal-subfields-T1T2 attached
>
> If anyone has had the same problem, could you please tell me how to solve
> it?
> And if I am doing something wrong, please tell me the correct way so I can
> continue with the analysis.
>
>
>
> Thank you!
>
> Renata
>
> ___
> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

[Krieger, Donald N.]

Hi Renata,

Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/

HTH - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Vaz pandolfo, 
Renata
Sent: Thursday, July 07, 2016 8:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

Dear FreeSurfer developers,
I am running recon-all on a healthy subject and I am also trying to get the 
hippocampal subfields segmentation.
On the mri directory there is no hippocampus output, and the recon-all exited 
with errors.
From my understanding, the error is with the lh.BA1_exvivo.label:

SUBJECTS_DIR
/home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading 
/home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label

The command I used was:
recon-all -all \
-i 
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
 -s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
-T2pial -hippocampal-subfields-T1


When trying to solve the problem, I noticed that I could have run a separate 
command for the hippocampal subfields and I ran this one:

recon-all \
-s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-hippocampal-subfields-T1T2 
~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz
  20110815_T2
Since the previous data had errors, I didn't really expect this to work, but I 
tried it anyways.
It exited "without errors", but on the log there was the following error twice:

Error:Cannot find CTF archive 
/usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
Extra info:
Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 
2016 x86_64 x86_64 x86_64 GNU/Linux
logs: recon-all and hippocampal-subfields-T1T2 attached
If anyone has had the same problem, could you please tell me how to solve it?
And if I am doing something wrong, please tell me the correct way so I can 
continue with the analysis.

Thank you!
Renata
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dispose of the e-mail.

Re: [Freesurfer] Recon all exited with error

[Bruce Fischl]

Hi Hassan

you need to look at the lh.orig.nofix and the lh.inflated.nofix to see what 
is going on. Typically this happens if there is some massive topological 
defect caused by e.g. the skull or cerebellum being attached to the wm.


cheers
Bruce


On Sat, 25 Apr 2015, Hassan 
bakhshi wrote:



Hi,
I was running 6 individual and all six couldn't finish at the Fix Topology
lh . 

I ran them again but again at this stage they got error.

the status file is attached.  

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