Re: [Freesurfer] Problem running recon-all

[fsbuild]

External Email - Use Caution

If you use a shared drive that is formatted in a way that is not 
compatible with the linux (ext3, ext4) file system, e.g., a shared windows 
drive, then running the linux software is not expected to work. A Windows 
file system does not support soft links, permissions etc. which means recon-all 
will fail when it tries to use soft links to point to files. So 
SUBJECTS_DIR has to point to a directory you can write to (on a linux file 
system).Similarly, the linux packaging tools (apt, dpkg, yum, 
rpm) expect to install Freesurfer on to a linux file system in order to set 
permissions, etc.
- R.

On Apr 23, 2024, at 11:50, Gregory Book gregory.a.b...@gmail.com 
wrote:External Email - Use 
CautionI did not see that 
message, which is why I posted again. Sorry about that!I will try using the 
package installer. We're using the .tar.gz method because it is located on a 
shared drive, but maybe we'll just need to install it locally if that works.On 
Tue, Apr 23, 2024 at 11:23 AM fsbuild fsbu...@contbay.com 
wrote:Did you try the instructions you were sent yesterday to run 
the actual installer and not use the tar file (which is not an installer) ?- 
R.I would try downloading and running the actual package 
installer,MailScanner has detected a possible fraud attempt from 
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 to the target system.. Then change directories to where you downloaded 
the package and try,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debI 
cannot guarantee the installer will work as the Debian linux packaging tools 
may find requirements in the Ubuntu package they cannot resolve/satisfy on your 
Debian system. We don’t test on debian linux. But the installer 
should notify you if it fails and why that is.On 4/23/24 09:21, Gregory Book 
(gregory.a.b...@gmail.com) 
wrote:External Email - Use 
CautionI recently installed 
freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When 
running recon-all, I get the following error:-bash: 
/opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file 
not foundPaths are all set, and all scripts and executables have execute 
permissions.What might be 
happening?___
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Re: [Freesurfer] Problem running recon-all

[Gregory Book]

External Email - Use Caution

I did not see that message, which is why I posted again. Sorry about that!
I will try using the package installer. We're using the .tar.gz method
because it is located on a shared drive, but maybe we'll just need to
install it locally if that works.

On Tue, Apr 23, 2024 at 11:23 AM fsbuild  wrote:

>
> Did you try the instructions  you were sent yesterday to run the actual
> installer and not use the tar file (which is not an installer) ?
>
> - R.
>
> I would try downloading and running the actual package installer,
>
>
> https://secure-web.cisco.com/1HKiItqb5Mbre7Zh9wBla2EeSBdrUlDXryrzl69LkLYWblBErmMFIQQrfAMG0IRSf5qYRXiqLgAvxJ7hiHx31g3l5g8FV2BkFnHs3RGzcu7zuuOC7I8pJBrfxRyYIv5iKV-gp6sds9DH_hHTpLBP0gBFEUSc2NLLNO5Ouh-l2ZwyxNIyZ7D49U0pu0Vp_Jk1wARFlwU08uGKnDp_fQEy65AtwuZAvhzTmxwbFhVqjikdZGvH06c-6dboQip0HbcHfOykTHHyFgVTKOrNun21Hj-dmU-SZLt8xKCUfS84tJvSzHKAW5YjEOR98r64hu_z-l7zVRRqA76SrlukfJD_hew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
>
>
> on to the target system..  Then change directories to where you downloaded
> the package and try,
>
> $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
>
> I cannot guarantee the installer will work as the Debian linux packaging
> tools may find requirements in the Ubuntu package they cannot
> resolve/satisfy on your Debian system.  We don’t test on debian linux.  But
> the installer should notify you if it fails and why that is.
>
>
>
> On 4/23/24 09:21, Gregory Book (gregory.a.b...@gmail.com) wrote:
>
> External Email - Use Caution
> I recently installed freesurfer 7.4.1 on a Debian 12 system (using the
> Ubuntu 22 .tar.gz). When running recon-all, I get the following error:
>
> -bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute:
> required file not found
>
> Paths are all set, and all scripts and executables have execute
> permissions.
> What might be happening?
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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 
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Re: [Freesurfer] Problem running recon-all

[fsbuild]

External Email - Use Caution



Did you try the instructions you were sent yesterday to run the actual 
installer and not use the tar file (which is not an installer) ?

  

- R.

  

  I would try downloading and running the actual package installer,



https://secure-web.cisco.com/1mB3zzEt6hQJ2VvtNrO3nW8sgR7_P581WGaaGeCTSIwiN-Z-x8Mtw6Z5nF23uvW00XlyjmsjQtPTwUkHji_2-9LmsBV2L2NfcLNBFy1Gsw0HvQ045CqPAZjAVhMRFnyyvnfw4xOPMnU-gIj1bM4eLgNASRmckkz7PGd6j28HxgvfDZkF1VK3pZSwTcISKqhKHuNQatTZ9vZjaWbY5k7I5N6dvIOuntBKrq-p5rjI7Q9G73EQ-rCrhQLcAOOyFsAtGAF4BJS1Ph12Iri8OA0T7HkE4bJHEf8g0Rde3zzo82KH1VslH5icbSMuRfXtKveMgAUF6jySJNeW6klBJSbUdsw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb


on to the target system. Then change directories to where you 
downloaded the package and try,


$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb



I
 cannot guarantee the installer will work as the Debian linux packaging 
tools may find requirements in the Ubuntu package they cannot 
resolve/satisfy on your Debian system. We don’t test on debian 
linux. 
But the installer should notify you if it fails and why that is.


  
  



On 4/23/24 09:21, Gregory Book (gregory.a.b...@gmail.com) wrote:



  External Email - Use 
Caution
  I recently installed freesurfer 7.4.1 on a Debian 12 
system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the 
following error:
-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required 
file not found

Paths are all set, and all scripts and executables have execute 
permissions.What might be happening?

  

  
  ___
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Re: [Freesurfer] Problem running recon-all

[Gregory Book]

External Email - Use Caution

I also see this error which is sent to stderr:
/usr/bin/time: cannot run recon-all: No such file or directory
It seems to be something related to the time command (or bash keyword)


Is your Freesurfer Environment sourced correctly?  Here is the wiki
help 
https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNgMM75HegbbUkTZoxL85vJjghWDwtg3Jjv4lsG0VZCTZ7YlhPuRczAQuIz8jePrWEIPQwVyAzcYv98U1CgmMpRUs3NZobucvYycgHFiqQk2sbCWslDa4-IfTbm2n-MTOjXS2Ej1uEpNgZ9lfvkJzcnj7SR5NRRe89nzPhY3jV3X1RPryu31aaVnBfDV7xeQ-b5WO6aR70li-RGAhVttoiUOo_E_Pj4-motaxaqZfNAhXYFAezM4dVSZlRAPrkwuMJG-Op02Vd54RwqKG-0U9qMFpYXqv7SLkSpIzyjUtjEw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux

Best,

Yujing
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Re: [Freesurfer] Problem running recon-all

[Gregory Book]

External Email - Use Caution

Yes, it's all sourced correctly. The output after sourcing:


bash:/opt/freesurfer/freesurfer-7.4.1$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /opt/freesurfer/freesurfer-7.4.1
FSFAST_HOME   /opt/freesurfer/freesurfer-7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /opt/freesurfer/freesurfer-7.4.1/subjects
MNI_DIR   /opt/freesurfer/freesurfer-7.4.1/mni




Is your Freesurfer Environment sourced correctly?  Here is the wiki
help 
https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNgMM75HegbbUkTZoxL85vJjghWDwtg3Jjv4lsG0VZCTZ7YlhPuRczAQuIz8jePrWEIPQwVyAzcYv98U1CgmMpRUs3NZobucvYycgHFiqQk2sbCWslDa4-IfTbm2n-MTOjXS2Ej1uEpNgZ9lfvkJzcnj7SR5NRRe89nzPhY3jV3X1RPryu31aaVnBfDV7xeQ-b5WO6aR70li-RGAhVttoiUOo_E_Pj4-motaxaqZfNAhXYFAezM4dVSZlRAPrkwuMJG-Op02Vd54RwqKG-0U9qMFpYXqv7SLkSpIzyjUtjEw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Gregory Book
Sent: Tuesday, April 23, 2024 9:21 AM
To: freesurfer 
Subject: [Freesurfer] Problem running recon-all


External Email - Use Caution
I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu
22 .tar.gz). When running recon-all, I get the following error:

-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required
file not found

Paths are all set, and all scripts and executables have execute permissions.
What might be happening?

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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] Problem running recon-all

[Huang, Yujing]

Is your Freesurfer Environment sourced correctly?  Here is the wiki help 
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Gregory Book
Sent: Tuesday, April 23, 2024 9:21 AM
To: freesurfer 
Subject: [Freesurfer] Problem running recon-all


External Email - Use Caution
I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 
22 .tar.gz). When running recon-all, I get the following error:

-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required 
file not found

Paths are all set, and all scripts and executables have execute permissions.
What might be happening?
___
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. 

[Freesurfer] Problem running recon-all

[Gregory Book]

External Email - Use Caution

I recently installed freesurfer 7.4.1 on a Debian 12 system (using the
Ubuntu 22 .tar.gz). When running recon-all, I get the following error:

-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute:
required file not found

Paths are all set, and all scripts and executables have execute permissions.
What might be happening?
___
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 
 .
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] Problem with recon-all --> nii.gz file not found

[Livia Ruehr]

External Email - Use Caution

It's running! I'll let you know if it stops again, but it works right now, 
after switching -sd and -i 


Thanks a lot!

Livia


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Dierker, Donna 

Gesendet: Freitag, 13. Januar 2023 16:27:17
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution

-i needs to be followed by the input volume
Move /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz right after -i.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Livia Ruehr 

Sent: Friday, January 13, 2023 9:15 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


* External Email - Caution *


External Email - Use Caution

Hey again,

sorry for my many problems, but this did not work as well (same error)

$ recon-all -s sub-04 -i -sd /home/lirh717c/Desktop/V5LGN/ 
/home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-08 -i -sd /home/lirh717c/Desktop/V5LGN/ 
/home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-19 -i -sd /home/lirh717c/Desktop/V5LGN/ 
/home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all
ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-04 exited with ERRORS at Fri Jan 13 16:12:12 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1fcbJ1EvfNsrLoS_-4-XxVI7CUvE1O75cdEGccFKmSsXPZXjuLI8OqcACMvkwryW1QeIw-malzbrMZYI7QOD4uwdJ2a8xmvEQ8BkSOeIhsOAAtckLiJCCZY6Bc8uhCqBpGNtA9BR2qpB9nSe-IoSClUA6yiTdptLGEE9p1Bidj6qGnCu8NhXSZd6U4disY19fL5pmRwQij6ZwUBNff84K-tGELiWGuetGF8B_dU7wif96nuAu6WvIAAYpFJs-z6MufGKrldE-OHBHeumP8pwHfaCqt5Wp1PaP1rBSfacIP-7KKM_HvUpWv_x3PFUToe94B6SiujHXLj_vs4brKtGVmg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-08 exited with ERRORS at Fri Jan 13 16:12:13 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1fcbJ1EvfNsrLoS_-4-XxVI7CUvE1O75cdEGccFKmSsXPZXjuLI8OqcACMvkwryW1QeIw-malzbrMZYI7QOD4uwdJ2a8xmvEQ8BkSOeIhsOAAtckLiJCCZY6Bc8uhCqBpGNtA9BR2qpB9nSe-IoSClUA6yiTdptLGEE9p1Bidj6qGnCu8NhXSZd6U4disY19fL5pmRwQij6ZwUBNff84K-tGELiWGuetGF8B_dU7wif96nuAu6WvIAAYpFJs-z6MufGKrldE-OHBHeumP8pwHfaCqt5Wp1PaP1rBSfacIP-7KKM_HvUpWv_x3PFUToe94B6SiujHXLj_vs4brKtGVmg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-19 exited with ERRORS at Fri Jan 13 16:12:13 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1fcbJ1EvfNsrLoS_-4-XxVI7CUvE1O75cdEGccFKmSsXPZXjuLI8OqcACMvkwryW1QeIw-malzbrMZYI7QOD4uwdJ2a8xmvEQ8BkSOeIhsOAAtckLiJCCZY6Bc8uhCqBpGNtA9BR2qpB9nSe-IoSClUA6yiTdptLGEE9p1Bidj6qGnCu8NhXSZd6U4disY19fL5pmRwQij6ZwUBNff84K-tGELiWGuetGF8B_dU7wif96nuAu6WvIAAYpFJs-z6MufGKrldE-OHBHeumP8pwHfaCqt5Wp1PaP1rBSfacIP-7KKM_HvUpWv_x3PFUToe94B6SiujHXLj_vs4brKtGVmg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting


I hope the file attached is the logfile? There is no .log- file in my 
freesurfer directory, maybe you could tell me where to find it.

Best wishes
Livia



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Huang, Yujing 

Gesendet: Freitag, 13. Januar 2023 15:49:30
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


Sorry for all the troubles.



‘-sd /home/lirh717c/Desktop/V5LGN/’ needs to be added to your recon-all command 
line. I see you only have ‘-sd’ added.



Can you attach recon-all.log if you continue to have problems?



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Friday, January 13, 2023 9:43 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found



External Email - Use Caution

Hello,



I've tried the echo command, which didn't work. Afterwards I tried -sd:



recon-all -s sub-04 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-08 -i -sd /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; 
recon-all -s sub-19 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all



It created the following:

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-04 exited with ERRORS at Fri Jan 13 15:38:54 CET 20

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Dierker, Donna]

External Email - Use Caution

-i needs to be followed by the input volume
Move /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz right after -i.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Livia Ruehr 

Sent: Friday, January 13, 2023 9:15 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


* External Email - Caution *

External Email - Use Caution

Hey again,

sorry for my many problems, but this did not work as well (same error)

$ recon-all -s sub-04 -i -sd /home/lirh717c/Desktop/V5LGN/ 
/home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-08 -i -sd /home/lirh717c/Desktop/V5LGN/ 
/home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-19 -i -sd /home/lirh717c/Desktop/V5LGN/ 
/home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all
ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-04 exited with ERRORS at Fri Jan 13 16:12:12 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/18pDo7SlDah8_pPzecRPLo8h4mHIBFpQmP2QjL1qYv_575Z7uVXIYVJLWIEztHJ0Yr87pu0YTrp5mw162M6xtJq3AXK5e0PnA27ZIQ5GRDpkIE8ACISN2uFN-rjM9_xil_Hs2NdjY7z-AcFsM93nyDAyqxrSufGxiAcS1GbHelZu6wHCPjCkuiG0e-g8ZjIwUBZfzhFdrLUuLs_oxhzB4Ig4rjUWKMwk6KuHZ7rXk4P869o3RQ8f7Vaz_drZX-xbgaVkB5GD3uQmFgIgnZvwBPjLKjADJCFCW4xIRolnHBw8jyt3ww9lLrTvTZfxxK7vIgVNcOq2RIS3L9UkEq2hpvw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-08 exited with ERRORS at Fri Jan 13 16:12:13 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/18pDo7SlDah8_pPzecRPLo8h4mHIBFpQmP2QjL1qYv_575Z7uVXIYVJLWIEztHJ0Yr87pu0YTrp5mw162M6xtJq3AXK5e0PnA27ZIQ5GRDpkIE8ACISN2uFN-rjM9_xil_Hs2NdjY7z-AcFsM93nyDAyqxrSufGxiAcS1GbHelZu6wHCPjCkuiG0e-g8ZjIwUBZfzhFdrLUuLs_oxhzB4Ig4rjUWKMwk6KuHZ7rXk4P869o3RQ8f7Vaz_drZX-xbgaVkB5GD3uQmFgIgnZvwBPjLKjADJCFCW4xIRolnHBw8jyt3ww9lLrTvTZfxxK7vIgVNcOq2RIS3L9UkEq2hpvw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-19 exited with ERRORS at Fri Jan 13 16:12:13 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/18pDo7SlDah8_pPzecRPLo8h4mHIBFpQmP2QjL1qYv_575Z7uVXIYVJLWIEztHJ0Yr87pu0YTrp5mw162M6xtJq3AXK5e0PnA27ZIQ5GRDpkIE8ACISN2uFN-rjM9_xil_Hs2NdjY7z-AcFsM93nyDAyqxrSufGxiAcS1GbHelZu6wHCPjCkuiG0e-g8ZjIwUBZfzhFdrLUuLs_oxhzB4Ig4rjUWKMwk6KuHZ7rXk4P869o3RQ8f7Vaz_drZX-xbgaVkB5GD3uQmFgIgnZvwBPjLKjADJCFCW4xIRolnHBw8jyt3ww9lLrTvTZfxxK7vIgVNcOq2RIS3L9UkEq2hpvw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting


I hope the file attached is the logfile? There is no .log- file in my 
freesurfer directory, maybe you could tell me where to find it.

Best wishes
Livia



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Huang, Yujing 

Gesendet: Freitag, 13. Januar 2023 15:49:30
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


Sorry for all the troubles.



‘-sd /home/lirh717c/Desktop/V5LGN/’ needs to be added to your recon-all command 
line. I see you only have ‘-sd’ added.



Can you attach recon-all.log if you continue to have problems?



Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Friday, January 13, 2023 9:43 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found



External Email - Use Caution

Hello,



I've tried the echo command, which didn't work. Afterwards I tried -sd:



recon-all -s sub-04 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-08 -i -sd /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; 
recon-all -s sub-19 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all



It created the following:

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-04 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/18pDo7SlDah8_pPzecRPLo8h4mHIBFpQmP2QjL1qYv_575Z7uVXIYVJLWIEztHJ0Yr87pu0YTrp5mw162M6xtJq3AXK5e0PnA27ZIQ5GRDpkIE8ACISN2uFN-rjM9_xil_Hs2NdjY7z-AcFsM93nyDAyqxrSufGxiAcS1GbHelZu6wHCPjCkuiG0e-g8ZjIwUBZfzhFdrLUuLs_oxhzB4Ig4rjUWKMwk6KuHZ7rXk4

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Huang, Yujing]

Sorry for all the troubles.

'-sd /home/lirh717c/Desktop/V5LGN/' needs to be added to your recon-all command 
line. I see you only have '-sd' added.

Can you attach recon-all.log if you continue to have problems?

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Friday, January 13, 2023 9:43 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Hello,

I've tried the echo command, which didn't work. Afterwards I tried -sd:

recon-all -s sub-04 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-08 -i -sd /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; 
recon-all -s sub-19 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

It created the following:

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-04 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-08 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-19 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

As I've said, I've tried everything now. Normally, it always worked after 
setting

  1.  FREESURFER_HOME=/path
  2.  SUBJECTS_DIR=/Subjectdirectorypath
  3.  souce FREESURFER_HOME=SetUpFreeSurfer.sh

and then I've ran recon-all with just the subject names.. Now, even if adding 
the path, it does not find my subjects dir. anymore.

Best wishes
Livia

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Gesendet: Freitag, 13. Januar 2023 15:30:51
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

I'm not sure why your $SUBJECTS_DIR is not recognized.

In the same terminal window,
1. echo $SUBJECTS_DIR
2. submit your recon-all

If this doesn't work, you can use -sd flag as suggested. In you case, add '-sd 
/home/lirh717c/Desktop/V5LGN/' to your recon-all.

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 Livia Ruehr
Sent: Friday, January 13, 2023 7:40 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Hi,

I've tried it today with the path in the command line:

recon-all -s sub-04 -i /home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz 
-all ; recon-all -s sub-08 -i 
/home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-19 -i /home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

However, it returns the following error (again):

ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag

I asked for showing up my subjects directory, which returns the following 
(correctly):

lirh717c@bam7-mint-chel:/freesurfer$ $SUBJECTS_DIR
bash: /home/lirh717c/Desktop/V5LGN: Is a directory
I do not understand what could still cause the problems...



Thank you so much in advance!

Best

Livia


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Gesendet: Donnerstag, 12. Januar 2023 18:25:58
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii.gz in the command.

SUBJECTS_DIR is not used to find images specified in recon-all command l

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Livia Ruehr]

External Email - Use Caution

Hello,

I've tried the echo command, which didn't work. Afterwards I tried -sd:

recon-all -s sub-04 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-08 -i -sd /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; 
recon-all -s sub-19 -i -sd 
/home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

It created the following:

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-04 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1ddYTy0U3ZM9lBC-HjXYl9v7BNd9JAukCGI6h00SFWi45DKnf0zcqye19kK4P0t6mMRbQT7Ki0ZKPMZYcuFqf3bgmzb3oHxGYfpY93Um4LItLOZDUwcOEX2o_CyrV63_M59XXj_0COV8s9waFtwnx6DeeV1YBPQGx3TJTpwZQJW5Rdkn9mzDiiZvm2cbI2SXwtHAEMKTxFmqPdo-_e2whDIVAC2HpybHlxAJdY_vvoCMEHOSsALnBYs6iLCdaGg0iktrdVDh8bzsMehByUfP1Am6gfaxZIWbsiTb1XBG_n43fhNJ-jvSpk0qSix_bu2WC/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-08 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1ddYTy0U3ZM9lBC-HjXYl9v7BNd9JAukCGI6h00SFWi45DKnf0zcqye19kK4P0t6mMRbQT7Ki0ZKPMZYcuFqf3bgmzb3oHxGYfpY93Um4LItLOZDUwcOEX2o_CyrV63_M59XXj_0COV8s9waFtwnx6DeeV1YBPQGx3TJTpwZQJW5Rdkn9mzDiiZvm2cbI2SXwtHAEMKTxFmqPdo-_e2whDIVAC2HpybHlxAJdY_vvoCMEHOSsALnBYs6iLCdaGg0iktrdVDh8bzsMehByUfP1Am6gfaxZIWbsiTb1XBG_n43fhNJ-jvSpk0qSix_bu2WC/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

ERROR: cannot find -sd
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-19 exited with ERRORS at Fri Jan 13 15:38:54 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1ddYTy0U3ZM9lBC-HjXYl9v7BNd9JAukCGI6h00SFWi45DKnf0zcqye19kK4P0t6mMRbQT7Ki0ZKPMZYcuFqf3bgmzb3oHxGYfpY93Um4LItLOZDUwcOEX2o_CyrV63_M59XXj_0COV8s9waFtwnx6DeeV1YBPQGx3TJTpwZQJW5Rdkn9mzDiiZvm2cbI2SXwtHAEMKTxFmqPdo-_e2whDIVAC2HpybHlxAJdY_vvoCMEHOSsALnBYs6iLCdaGg0iktrdVDh8bzsMehByUfP1Am6gfaxZIWbsiTb1XBG_n43fhNJ-jvSpk0qSix_bu2WC/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting

As I've said, I've tried everything now. Normally, it always worked after 
setting

  1.  FREESURFER_HOME=/path
  2.  SUBJECTS_DIR=/Subjectdirectorypath
  3.  souce FREESURFER_HOME=SetUpFreeSurfer.sh

and then I've ran recon-all with just the subject names.. Now, even if adding 
the path, it does not find my subjects dir. anymore.

Best wishes
Livia

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Huang, Yujing 

Gesendet: Freitag, 13. Januar 2023 15:30:51
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

I’m not sure why your $SUBJECTS_DIR is not recognized.

In the same terminal window,
1. echo $SUBJECTS_DIR
2. submit your recon-all

If this doesn’t work, you can use -sd flag as suggested. In you case, add ‘-sd 
/home/lirh717c/Desktop/V5LGN/’ to your recon-all.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Friday, January 13, 2023 7:40 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Hi,

I've tried it today with the path in the command line:

recon-all -s sub-04 -i /home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz 
-all ; recon-all -s sub-08 -i 
/home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-19 -i /home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

However, it returns the following error (again):

ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag

I asked for showing up my subjects directory, which returns the following 
(correctly):

lirh717c@bam7-mint-chel:/freesurfer$ $SUBJECTS_DIR
bash: /home/lirh717c/Desktop/V5LGN: Is a directory
I do not understand what could still cause the problems...



Thank you so much in advance!

Best

Livia


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harv

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Huang, Yujing]

Hi Livia,

I'm not sure why your $SUBJECTS_DIR is not recognized.

In the same terminal window,
1. echo $SUBJECTS_DIR
2. submit your recon-all

If this doesn't work, you can use -sd flag as suggested. In you case, add '-sd 
/home/lirh717c/Desktop/V5LGN/' to your recon-all.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Friday, January 13, 2023 7:40 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Hi,

I've tried it today with the path in the command line:

recon-all -s sub-04 -i /home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz 
-all ; recon-all -s sub-08 -i 
/home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-19 -i /home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

However, it returns the following error (again):

ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag

I asked for showing up my subjects directory, which returns the following 
(correctly):

lirh717c@bam7-mint-chel:/freesurfer$ $SUBJECTS_DIR
bash: /home/lirh717c/Desktop/V5LGN: Is a directory
I do not understand what could still cause the problems...



Thank you so much in advance!

Best

Livia


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Gesendet: Donnerstag, 12. Januar 2023 18:25:58
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii.gz in the command.

SUBJECTS_DIR is not used to find images specified in recon-all command line.

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 Livia Ruehr
Sent: Thursday, January 12, 2023 12:06 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Dear Yujing,

Thank your for your fast reply. So you mean that I need to paste the whole path 
(home/../../..) before the name of the .nii.gz file in the command ?

It is weird, because I have always used it as sent and it worked until today. 
My subjects directory (called V5LGN, see mail below) contains all compressed 
nifti files of my subjects and additional output directories of the 
successfully processed subjects. This is why I thought that with the 
specification of SUBJECTS _DIR freesurfer knows where the subjects called are 
since they are there on this level without any subdirectories...?

Best
Livia

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Gesendet: Donnerstag, 12. Januar 2023 17:53:41
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

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 Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I w

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Livia Ruehr]

External Email - Use Caution

Hi,

I've tried it today with the path in the command line:

recon-all -s sub-04 -i /home/lirh717c/Desktop/V5LGN/sub-04-ses-01_T1w.nii.gz 
-all ; recon-all -s sub-08 -i 
/home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz -all ; recon-all -s 
sub-19 -i /home/lirh717c/Desktop/V5LGN/sub-19-ses-01_T1w.nii.gz -all

However, it returns the following error (again):

ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag
ERROR: environment variable SUBJECTS_DIR not set
  this can be done by setting it in the shell before
  executing recon-all or by using the -sd flag

I asked for showing up my subjects directory, which returns the following 
(correctly):

lirh717c@bam7-mint-chel:/freesurfer$ $SUBJECTS_DIR
bash: /home/lirh717c/Desktop/V5LGN: Is a directory

I do not understand what could still cause the problems...


Thank you so much in advance!

Best

Livia


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Huang, Yujing 

Gesendet: Donnerstag, 12. Januar 2023 18:25:58
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii.gz in the command.

SUBJECTS_DIR is not used to find images specified in recon-all command line.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 12:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Dear Yujing,

Thank your for your fast reply. So you mean that I need to paste the whole path 
(home/../../..) before the name of the .nii.gz file in the command ?

It is weird, because I have always used it as sent and it worked until today. 
My subjects directory (called V5LGN, see mail below) contains all compressed 
nifti files of my subjects and additional output directories of the 
successfully processed subjects. This is why I thought that with the 
specification of SUBJECTS _DIR freesurfer knows where the subjects called are 
since they are there on this level without any subdirectories...?

Best
Livia

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Gesendet: Donnerstag, 12. Januar 2023 17:53:41
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

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 Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/1BVn9BnqxhmQnP3cf1l8y4vH65NjoAmpm1eAGtcMWdiAAaR7lhfgcuEspTEEKKdUgOU4K1BTEJwECumRM8eIg7b-xsiZ0Sh8cpPE3WJ6xjr0Ac8-pIpxuGstNbig-VWb5rFo0vLn0hCDkDtKlyrAZLTUEHNqDj1Jb1CBrmgw82w4i_sdturQrGDzIgRaeGtgmmQwIcxvzIbU3DQ4e9bGkihsya2fHokb8rhC66etH3dWPvCdP8uz-

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Huang, Yujing]

Hi Livia,

Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii.gz in the command.

SUBJECTS_DIR is not used to find images specified in recon-all command line.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 12:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Dear Yujing,

Thank your for your fast reply. So you mean that I need to paste the whole path 
(home/../../..) before the name of the .nii.gz file in the command ?

It is weird, because I have always used it as sent and it worked until today. 
My subjects directory (called V5LGN, see mail below) contains all compressed 
nifti files of my subjects and additional output directories of the 
successfully processed subjects. This is why I thought that with the 
specification of SUBJECTS _DIR freesurfer knows where the subjects called are 
since they are there on this level without any subdirectories...?

Best
Livia

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Gesendet: Donnerstag, 12. Januar 2023 17:53:41
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

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 Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<http://secure-web.cisco.com/188SCSXJL6xo2VGEo8HgYHx-r8WYg6qIHHBrJ5H8jADmFD7EkFuJdKFoqlV-t-VuYAfJbSFMnLOrvu_BlGnmpk4fgygDqyDiV64_LMs61QU9jtUqb0B-Uqqoe5kMGs7yZDpO1ga8B5uXjs_T5a5SzUNvszvbEXgdSW53Pn6gW4T02RH4C5SUwaUhhZ0JZuFdJdvOuf7iSsdGNzXNpjNVoVL5fgwVDUzSAuyTypmUncNw7WmScPwsSuHAfjOw4V_GRigrasjDayhnpCVqPiuf6ip6Exro1m5L9PVxaiNL6tcdHHEHcwHyFlgGzahojKSo2HNFTQuGSWiFcieUr-Wlb-Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>



This applies not only to one file, but for all of them. I have also tried to 
rerun recon-all of another file that had been successful in december, I have 
also copied and renamed it to not overwrite it.. but none of the data sets were 
found!



For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the 
source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR

 freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME   /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lirh717c/Desktop/V5LGN
MNI_DIR   /freesurfer/mni



After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my 
files. Additionally, I can open freesurfer now and open

the scans within freeview, so that the following appears to me:

- my data are okay and I can open them

- freesurfer is generally running (only thing is one warning: (process:3965): 
Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Livia Ruehr]

External Email - Use Caution

Dear Yujing,

Thank your for your fast reply. So you mean that I need to paste the whole path 
(home/../../..) before the name of the .nii.gz file in the command ?

It is weird, because I have always used it as sent and it worked until today. 
My subjects directory (called V5LGN, see mail below) contains all compressed 
nifti files of my subjects and additional output directories of the 
successfully processed subjects. This is why I thought that with the 
specification of SUBJECTS _DIR freesurfer knows where the subjects called are 
since they are there on this level without any subdirectories...?

Best
Livia

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Huang, Yujing 

Gesendet: Donnerstag, 12. Januar 2023 17:53:41
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/188SCSXJL6xo2VGEo8HgYHx-r8WYg6qIHHBrJ5H8jADmFD7EkFuJdKFoqlV-t-VuYAfJbSFMnLOrvu_BlGnmpk4fgygDqyDiV64_LMs61QU9jtUqb0B-Uqqoe5kMGs7yZDpO1ga8B5uXjs_T5a5SzUNvszvbEXgdSW53Pn6gW4T02RH4C5SUwaUhhZ0JZuFdJdvOuf7iSsdGNzXNpjNVoVL5fgwVDUzSAuyTypmUncNw7WmScPwsSuHAfjOw4V_GRigrasjDayhnpCVqPiuf6ip6Exro1m5L9PVxaiNL6tcdHHEHcwHyFlgGzahojKSo2HNFTQuGSWiFcieUr-Wlb-Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting



This applies not only to one file, but for all of them. I have also tried to 
rerun recon-all of another file that had been successful in december, I have 
also copied and renamed it to not overwrite it.. but none of the data sets were 
found!



For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the 
source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR

 freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME   /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lirh717c/Desktop/V5LGN
MNI_DIR   /freesurfer/mni



After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my 
files. Additionally, I can open freesurfer now and open

the scans within freeview, so that the following appears to me:

- my data are okay and I can open them

- freesurfer is generally running (only thing is one warning: (process:3965): 
Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.

Using the fallback 'C' locale.)

- even if setting subjects directory to another directory, it is not working, 
the problem is neither the data nor the directory

- the subjects directory has correctly been set and I can access it --> my 
files are seen here

To this reason, I have no ideas anymore.

I am looking forward to your reply!



Kind regards

Livia Rühr

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Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Huang, Yujing]

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



This applies not only to one file, but for all of them. I have also tried to 
rerun recon-all of another file that had been successful in december, I have 
also copied and renamed it to not overwrite it.. but none of the data sets were 
found!



For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the 
source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR

 freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME   /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lirh717c/Desktop/V5LGN
MNI_DIR   /freesurfer/mni



After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my 
files. Additionally, I can open freesurfer now and open

the scans within freeview, so that the following appears to me:

- my data are okay and I can open them

- freesurfer is generally running (only thing is one warning: (process:3965): 
Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.

Using the fallback 'C' locale.)

- even if setting subjects directory to another directory, it is not working, 
the problem is neither the data nor the directory

- the subjects directory has correctly been set and I can access it --> my 
files are seen here

To this reason, I have no ideas anymore.

I am looking forward to your reply!



Kind regards

Livia Rühr

___
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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] Problem with recon-all command in tutorial dataset

[Tim Schäfer]

External Email - Use Caution

Try:

export TUTORIAL_DATA=/home/shao/tutorial_data

Tim

> On August 11, 2020 at 6:51 AM Wei Shao  wrote:
> 
> 
> External Email - Use Caution
> 
> Hi, Freesurfer Team
> 
> My name is Wei Shao, I just a beginner of Freesurfer. As I play around with
> the tutorial data, here is a problem I met, I tried to recon-all the dicoms
> data as the tutorial instruction practice with the date instructed, but it
> always reports like the SUBJECTS_DIR directory does not exist.
> 
> 
> [shao@WeiS ~]$ export TUTORIAL_DATA=tutorial_data
> [shao@WeiS ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data
> [shao@WeiS ~]$ cd $SUBJECTS_DIR/dicoms
> [shao@WeiS dicoms]$ recon-all -all -i I50 -s  Subj001
> ERROR: SUBJECTS_DIR tutorial_data/practice_with_data does not exist.
> [shao@WeiS dicoms]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>  freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> WARNING: tutorial_data/practice_with_data does not exist
> FREESURFER_HOME   /usr/local/freesurfer/7.1.0-1
> FSFAST_HOME   /usr/local/freesurfer/7.1.0-1/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  tutorial_data/practice_with_data
> MNI_DIR   /usr/local/freesurfer/7.1.0-1/mni
> [shao@WeiS dicoms]$ pwd
> /home/shao/tutorial_data/practice_with_data/dicoms
> [shao@WeiS dicoms]$
> 
> 
> What I should do to fix this problem, Thanks in advance.
> 
> Best,
> Wei
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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[Freesurfer] Problem with recon-all command in tutorial dataset

[Wei Shao]

External Email - Use Caution

Hi, Freesurfer Team

My name is Wei Shao, I just a beginner of Freesurfer. As I play around with
the tutorial data, here is a problem I met, I tried to recon-all the dicoms
data as the tutorial instruction practice with the date instructed, but it
always reports like the SUBJECTS_DIR directory does not exist.


[shao@WeiS ~]$ export TUTORIAL_DATA=tutorial_data
[shao@WeiS ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data
[shao@WeiS ~]$ cd $SUBJECTS_DIR/dicoms
[shao@WeiS dicoms]$ recon-all -all -i I50 -s  Subj001
ERROR: SUBJECTS_DIR tutorial_data/practice_with_data does not exist.
[shao@WeiS dicoms]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: tutorial_data/practice_with_data does not exist
FREESURFER_HOME   /usr/local/freesurfer/7.1.0-1
FSFAST_HOME   /usr/local/freesurfer/7.1.0-1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  tutorial_data/practice_with_data
MNI_DIR   /usr/local/freesurfer/7.1.0-1/mni
[shao@WeiS dicoms]$ pwd
/home/shao/tutorial_data/practice_with_data/dicoms
[shao@WeiS dicoms]$


What I should do to fix this problem, Thanks in advance.

Best,
Wei
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Re: [Freesurfer] Problem running recon-all example from installation guide

[Tim Schäfer]

External Email - Use Caution

Hi Andreas,

If you want to run recon-all on Bert, I would suggest to copy him to some place 
where you have write access and use that as the SUBJECTS_DIR. 

Running FreeSurfer as root is a bad idea and usually leads to trouble later 
(e.g., the output will also be owned by root instead of your user).

Something like this if you use the bash shell:

mkdir -p ~/data/bert_only/
cp -r /usr/local/freesurfer/subjects/bert ~/data/bert_only/
export SUBJECTS_DIR=~/data/bert_only
# now run recon-all

Best,

Tim

> On February 19, 2020 at 11:25 AM Andreas Vitikan  
> wrote:
> 
> 
> External Email - Use Caution
> 
> Hello,
> 
> I am trying to get the examples running as per the FreeSurfer installation
> guide.
> I initially got a recon-all not found error which turned out to be due to
> the lack of tcsh/csh, which I installed (I found this fix in the mailing
> list) and now get a different error.
> 
> mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert':
> Permission denied
> mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert':
> Permission denied
> mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert':
> Permission denied
> cp: cannot create regular file
> '/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such
> file or directory
> cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No
> such file or directory
> INFO: FreeSurfer build stamps do not match
> Subject Stamp:
> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> /usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file
> or directory.
> 
> I thought it might be related to permissions but running under sudo
> gives a different error. How do I fix this?
> 
> - Andreas V.
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-- 
Tim Schäfer

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[Freesurfer] Problem running recon-all example from installation guide

[Andreas Vitikan]

External Email - Use Caution

Hello,

I am trying to get the examples running as per the FreeSurfer installation
guide.
I initially got a recon-all not found error which turned out to be due to
the lack of tcsh/csh, which I installed (I found this fix in the mailing
list) and now get a different error.

mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert':
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert':
Permission denied
mkdir: cannot create directory '/usr/local/freesurfer/subjects/bert':
Permission denied
cp: cannot create regular file
'/usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt': No such
file or directory
cat: /usr/local/freesurfer/subjects/bert/scripts/build-stamp.txt: No
such file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
/usr/local/freesurfer/subjects/bert/scripts/patchdir.txt: No such file
or directory.

I thought it might be related to permissions but running under sudo
gives a different error. How do I fix this?

- Andreas V.
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Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

Several things:

1) The FreeSurfer list is probably not the best place for support for the
HCP Pipelines as there is a dedicated user list
hcp-us...@humanconnectome.org for this.  Folks who support the HCP
Pipelines may not monitor the FreeSurfer list as closely.
2) It is very difficult to follow these threads across multiple days when
the prior replies are not included in each e-mail.
3) it is correct that PreFreeSurfer does not use matlab.  It does use
python however, which you have gotten a bunch of python errors.  It would
appear that there is some incompatibility between Python and your mac¹s
installed libraries, which is used for gradient nonlinearity correction
and several FSL scripts.  Because of how your libraries are configured, it
appears to be looking for them in your matlab install, rather than in your
system libraries folders.  This library
"/Applications/MATLAB_R2017b.app/sys/os/maci64/libgfortran.3.dylib² is not
compatible with your scipy python 3.6 install.  Perhaps there is another
version of libgfortran.3 and you have defaulted your system to look for
this in matlab¹s folders before anywhere else.  This could occur if trying
to run the HCP Pipelines from inside matlab, which is not recommended.

Based on the above, you might get actually best get help on the FSL list
for this specific issue (entitled something like ³cannot run FSL python
code like /usr/local/fsl/bin/imcp on my mac, please see these errors
below²).

Matt.

On 2/17/19, 3:20 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Shachar Gal"  wrote:

>External Email - Use Caution
>
>Actually Im not really sure why Matlab pops up here.. this is ran there
>is nothing that is Matlab dependent in the PreFreesurfer Pipeline...
>
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Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

Actually Im not really sure why Matlab pops up here.. this is ran there is 
nothing that is Matlab dependent in the PreFreesurfer Pipeline...

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Re: [Freesurfer] problem using recon-all

[Hoopes, Andrew]

Is python being called from matlab here? It probably has to do with how matlab 
sets DYLD_LIBRARY_PATH. I would maybe try using pip to uninstall and reinstall 
the fslpython scipy package, but that might be dangerous - I’m not sure how fsl 
sets up its python env. I’ll look into it a bit more and get back to you
Andrew


From: Shachar Gal 
Date: Thursday, February 14, 2019 at 4:31 AM
To: "Hoopes, Andrew" , "ts...@rcmd.org" 
, FS Help 
Subject: Re: [Freesurfer] problem using recon-all


External Email - Use Caution
you can ignore the nifti errors in the beginning of the error message, because 
it was just a small glitch that I solved. the rest of the errors still stand, 
and are unclear to me..

On Thu, 14 Feb 2019 at 11:09, Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
Hey,
So I disabled SIP, and tried to run the subject from the beginning, and sadly I 
encountered an error while running the PreFreesurfer Pipeline, which worked 
fine until disabling SIP.
This is the error message:

** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslreorient2std: line 99: [: too many arguments
/usr/local/fsl/bin/fslreorient2std: line 108: [: =: unary operator expected
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
(standard_in) 1: parse error
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 107: [: =: unary operator expected
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot use RLAPSI notation for nifti files without either sform or qform set
Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: Not Averaging T1w 
Images
Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: ONLY ONE AVERAGE 
FOUND: COPYING
Traceback (most recent call last):
  File "/usr/local/fsl/bin/imcp", line 11, in 
load_entry_point('fslpy==1.7.0', 'console_scripts', 'imcp')()
  File 
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
 line 479, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
  File 
"/usr/local/fsl/f

Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

you can ignore the nifti errors in the beginning of the error message,
because it was just a small glitch that I solved. the rest of the errors
still stand, and are unclear to me..

On Thu, 14 Feb 2019 at 11:09, Shachar Gal  wrote:

> Hey,
> So I disabled SIP, and tried to run the subject from the beginning, and
> sadly I encountered an error while running the PreFreesurfer Pipeline,
> which worked fine until disabling SIP.
> This is the error message:
>
> ** ERROR (nifti_image_read): short header read
> '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
> ** ERROR:
> nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
> bad header info
> ERROR: failed to open file
> /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
> ERROR: Could not open file
> ** ERROR (nifti_image_read): short header read
> '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
> ** ERROR:
> nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
> bad header info
> ERROR: failed to open file
> /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
> ERROR: Could not open file
> /usr/local/fsl/bin/fslreorient2std: line 99: [: too many arguments
> /usr/local/fsl/bin/fslreorient2std: line 108: [: =: unary operator expected
> ** ERROR (nifti_image_read): short header read
> '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
> ** ERROR:
> nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
> bad header info
> ERROR: failed to open file
> /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
> ERROR: Could not open file
> (standard_in) 1: parse error
> ** ERROR (nifti_image_read): short header read
> '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
> ** ERROR:
> nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
> bad header info
> ERROR: failed to open file
> /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
> ERROR: Could not open file
> /usr/local/fsl/bin/fslswapdim: line 107: [: =: unary operator expected
> ** ERROR (nifti_image_read): short header read
> '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
> ** ERROR:
> nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
> bad header info
> ERROR: failed to open file
> /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
> ERROR: Could not open file
> /usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected
> ** ERROR (nifti_image_read): short header read
> '/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
> ** ERROR:
> nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
> bad header info
> ERROR: failed to open file
> /Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
> ERROR: Could not open file
> /usr/local/fsl/bin/fslswapdim: line 117: [: -gt: unary operator expected
> Cannot use RLAPSI notation for nifti files without either sform or qform
> set
> Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: Not Averaging T1w
> Images
> Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: ONLY ONE AVERAGE
> FOUND: COPYING
> Traceback (most recent call last):
>   File "/usr/local/fsl/bin/imcp", line 11, in 
> load_entry_point('fslpy==1.7.0', 'console_scripts', 'imcp')()
>   File
> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
> line 479, in load_entry_point
> return get_distribution(dist).load_entry_point(group, name)
>   File
> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
> line 2703, in load_entry_point
> return ep.load()
>   File
> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
> line 2321, in load
> return self.resolve()
>   File
> "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
> line 2327, in resolve
> module = 

Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

Hey,
So I disabled SIP, and tried to run the subject from the beginning, and sadly I 
encountered an error while running the PreFreesurfer Pipeline, which worked 
fine until disabling SIP.
This is the error message: 

** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslreorient2std: line 99: [: too many arguments
/usr/local/fsl/bin/fslreorient2std: line 108: [: =: unary operator expected
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
(standard_in) 1: parse error
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 107: [: =: unary operator expected
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected
** ERROR (nifti_image_read): short header read 
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR: 
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
 bad header info
ERROR: failed to open file 
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot use RLAPSI notation for nifti files without either sform or qform set
Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: Not Averaging T1w 
Images
Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: ONLY ONE AVERAGE 
FOUND: COPYING
Traceback (most recent call last):
  File "/usr/local/fsl/bin/imcp", line 11, in 
load_entry_point('fslpy==1.7.0', 'console_scripts', 'imcp')()
  File 
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
 line 479, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
  File 
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
 line 2703, in load_entry_point
return ep.load()
  File 
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
 line 2321, in load
return self.resolve()
  File 
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
 line 2327, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File 
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/scripts/imcp.py",
 line 26, in 
import fsl.utils.imcp as imcp
  File 
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/utils/imcp.py",
 line 24, in 
import fsl.data.image as fslimage
  File 

Re: [Freesurfer] problem using recon-all

[Hoopes, Andrew]

Hi Shachar, the patch will not fix this. You’ll probably need to disable SIP - 
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
 - which prevents access to libraries in /usr. This bug has been fixed in the 
dev version.

best
Andrew


From:  on behalf of Shachar Gal 

Reply-To: FS Help 
Date: Wednesday, February 13, 2019 at 9:24 AM
To: "ts...@rcmd.org" 
Cc: FS Help , Ido Tavor 
Subject: Re: [Freesurfer] problem using recon-all


External Email - Use Caution
I am not sure that the issue is with the SIP, because the message says this - 
"freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" does not exist in the patches 
directory, and in fact, it does not exist here - 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/
any ideas where this patch needs to come from?

thanks,
Shachar

On Wed, 13 Feb 2019 at 16:09, Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
Hey Tim,

I tried to run the “-E fs_update”, and got this message:

rsync -zbrlv --progress --suffix=.1550066275_bak 
rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
 /Applications/freesurfer
receiving file list ...
rsync: change_dir 
"/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in 
pub) failed: No such file or directory (2)
0 files to consider

sent 4 bytes  received 9 bytes  8.67 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files could not be transferred (code 23) at 
/BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404)
 [receiver=2.6.9]




Does the indicate I should disable SIP, or is it a different issue?

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

Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

I am not sure that the issue is with the SIP, because the message says this
- *"freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c"* does not exist in the
patches directory, and in fact, it does not exist here -
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/
any ideas where this patch needs to come from?

thanks,
Shachar

On Wed, 13 Feb 2019 at 16:09, Shachar Gal  wrote:

> Hey Tim,
>
> I tried to run the “-E fs_update”, and got this message:
>
> rsync -zbrlv --progress --suffix=.1550066275_bak
> rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
> /Applications/freesurfer
> receiving file list ...
> rsync: change_dir
> "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c"
> (in pub) failed: No such file or directory (2)
> 0 files to consider
>
> sent 4 bytes  received 9 bytes  8.67 bytes/sec
> total size is 0  speedup is 0.00
> rsync error: some files could not be transferred (code 23) at
> /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404)
> [receiver=2.6.9]
>
>
> Does the indicate I should disable SIP, or is it a different issue?
>
> Thanks,
> Shachar
>
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

Hey Tim,

I tried to run the “-E fs_update”, and got this message:

rsync -zbrlv --progress --suffix=.1550066275_bak 
rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
 /Applications/freesurfer
receiving file list ... 
rsync: change_dir 
"/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in 
pub) failed: No such file or directory (2)
0 files to consider

sent 4 bytes  received 9 bytes  8.67 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files could not be transferred (code 23) at 
/BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404)
 [receiver=2.6.9]


Does the indicate I should disable SIP, or is it a different issue?

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

Re: [Freesurfer] problem using recon-all

[Tim Schäfer]

External Email - Use Caution

That being said, this did not help in my case. I had to disable System 
Integrity Protection.

> On February 13, 2019 at 2:08 PM Tim Schäfer  wrote:
> 
> 
> External Email - Use Caution
> 
> The release notes mention this message:
> 
>   https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
> 
> under 'Known issues' and recommend you run 'sudo -E fs_update'.
> 
> 
> > On February 13, 2019 at 1:45 PM Shachar Gal  wrote:
> > 
> > 
> > External Email - Use Caution
> > 
> > ok, so I tried doing what I mentioned above (I used the hcp recon-all
> > version), and when trying to run the FreeSurfer Pipeline, I received this
> > error:
> > 
> > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> > 
> > dyld: Symbol not found: ___emutls_get_address
> >   Referenced from:
> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> >   Expected in: /usr/lib/libSystem.B.dylib
> > 
> > any thoughts?
> > 
> > thanks,
> > Shachar
> > 
> > 
> > 
> > On Wed, 13 Feb 2019 at 10:21, Shachar Gal  wrote:
> > 
> > > Hey Douglas,
> > > A couple of question about the patch
> > > In order to use it, I need to download the regular Freesurfer version-6,
> > > and replace only the scripts that are in the patch? (i.e
> > > Make_average_surface, recon_all, conf2hires, longmc)
> > > Which recon-all to use? The one under the hcp sub folder?
> > >
> > > Thanks!
> > > Shachar
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Tim
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
Tim

___
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Re: [Freesurfer] problem using recon-all

[Tim Schäfer]

External Email - Use Caution

The release notes mention this message:

  https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

under 'Known issues' and recommend you run 'sudo -E fs_update'.


> On February 13, 2019 at 1:45 PM Shachar Gal  wrote:
> 
> 
> External Email - Use Caution
> 
> ok, so I tried doing what I mentioned above (I used the hcp recon-all
> version), and when trying to run the FreeSurfer Pipeline, I received this
> error:
> 
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
> 
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
> 
> any thoughts?
> 
> thanks,
> Shachar
> 
> 
> 
> On Wed, 13 Feb 2019 at 10:21, Shachar Gal  wrote:
> 
> > Hey Douglas,
> > A couple of question about the patch
> > In order to use it, I need to download the regular Freesurfer version-6,
> > and replace only the scripts that are in the patch? (i.e
> > Make_average_surface, recon_all, conf2hires, longmc)
> > Which recon-all to use? The one under the hcp sub folder?
> >
> > Thanks!
> > Shachar
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Tim

___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

ok, so I tried doing what I mentioned above (I used the hcp recon-all
version), and when trying to run the FreeSurfer Pipeline, I received this
error:

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

any thoughts?

thanks,
Shachar



On Wed, 13 Feb 2019 at 10:21, Shachar Gal  wrote:

> Hey Douglas,
> A couple of question about the patch
> In order to use it, I need to download the regular Freesurfer version-6,
> and replace only the scripts that are in the patch? (i.e
> Make_average_surface, recon_all, conf2hires, longmc)
> Which recon-all to use? The one under the hcp sub folder?
>
> Thanks!
> Shachar
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

Hey Douglas,
A couple of question about the patch
In order to use it, I need to download the regular Freesurfer version-6, and 
replace only the scripts that are in the patch? (i.e Make_average_surface, 
recon_all, conf2hires, longmc)
Which recon-all to use? The one under the hcp sub folder?

Thanks!
Shachar

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Re: [Freesurfer] problem using recon-all

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

If you want to test it out yourself, you can get it from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/


On 2/4/19 6:09 AM, Glasser, Matthew wrote:
>
> External Email - Use Caution
>
> There is a little more testing we are doing.
>
> Matt.
>
> From: Shachar Gal mailto:gal.shac...@gmail.com>>
> Date: Monday, February 4, 2019 at 3:32 AM
> To: Matt Glasser mailto:glass...@wustl.edu>>
> Cc: Freesurfer support list  >, Ido Tavor 
> mailto:idota...@gmail.com>>
> Subject: Re: problem using recon-all
>
> hey,
> is there any update regarding the release of the FreeSurfer 6 
> HCP-compatible version?
>
> cheers,
> Shachar
>
> On Mon, 14 Jan 2019 at 14:58 Shachar Gal  > wrote:
>
> thanks,
> hope it'll work
> anyway, looking forward for the version 6 release
>
> cheers,
> Shachar
>
> On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew  > wrote:
>
> Ubuntu 14.04 should still work.
>
> Matt.
>
> From: Shachar Gal  >
> Date: Monday, January 14, 2019 at 5:43 AM
> To: Freesurfer support list  >, Matt Glasser
> mailto:glass...@wustl.edu>>, Ido Tavor
> mailto:idota...@gmail.com>>
> Subject: Re: problem using recon-all
>
> if the problem is with the versions, maybe downgrading my OS
> for now will do the trick? do you happen know what is the
> latest ubuntu that is compatible with the 5.3-HCP version?
> does this also occur in centOS?
>
> thanks
>
> On Sun, 13 Jan 2019 at 17:46 Shachar Gal
> mailto:gal.shac...@gmail.com>> wrote:
>
> hello,
> I using the HCP FreeSurfer Pipeline (using FreeSurfer
> 5.3-HCP version) on ubuntu, and I encounter this error
> (copying from the recon-all.log)
> ___
> #@# Talairach Sun Jan 13 17:35:07 IST 2019
> /home/shachar/piano_hcp/102/102/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
> --no-rescale --i orig.mgz --o orig_nu.mgz
>
> Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6
> 14:45:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08
> IST 2019 ___
>
> i'm a bit confused by the lack of error descriptions, and
> would appreciate any leads for solving it :)
>
> Shachar
>
> 
> 
>
> The materials in this message are private and may contain
> Protected Healthcare Information or other information of a
> sensitive nature. If you are not the intended recipient, be
> advised that any unauthorized use, disclosure, copying or the
> taking of any action in reliance on the contents of this
> information is strictly prohibited. If you have received this
> email in error, please immediately notify the sender via
> telephone or return mail.
>
> 
>
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying or the taking of any action in reliance on 
> the contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

There is a little more testing we are doing.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, February 4, 2019 at 3:32 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, Ido 
Tavor mailto:idota...@gmail.com>>
Subject: Re: problem using recon-all

hey,
is there any update regarding the release of the FreeSurfer 6 HCP-compatible 
version?

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:58 Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
thanks,
hope it'll work
anyway, looking forward for the version 6 release

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
Ubuntu 14.04 should still work.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, January 14, 2019 at 5:43 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, Matt 
Glasser mailto:glass...@wustl.edu>>, Ido Tavor 
mailto:idota...@gmail.com>>
Subject: Re: problem using recon-all

if the problem is with the versions, maybe downgrading my OS for now will do 
the trick? do you happen know what is the latest ubuntu that is compatible with 
the 5.3-HCP version?
does this also occur in centOS?

thanks

On Sun, 13 Jan 2019 at 17:46 Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on 
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

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

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 
___

i'm a bit confused by the lack of error descriptions, and would appreciate any 
leads for solving it :)

Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

hey,
is there any update regarding the release of the FreeSurfer 6
HCP-compatible version?

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:58 Shachar Gal  wrote:

> thanks,
> hope it'll work
> anyway, looking forward for the version 6 release
>
> cheers,
> Shachar
>
> On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew  wrote:
>
>> Ubuntu 14.04 should still work.
>>
>> Matt.
>>
>> From: Shachar Gal 
>> Date: Monday, January 14, 2019 at 5:43 AM
>> To: Freesurfer support list , Matt
>> Glasser , Ido Tavor 
>> Subject: Re: problem using recon-all
>>
>> if the problem is with the versions, maybe downgrading my OS for now will
>> do the trick? do you happen know what is the latest ubuntu that is
>> compatible with the 5.3-HCP version?
>> does this also occur in centOS?
>>
>> thanks
>>
>> On Sun, 13 Jan 2019 at 17:46 Shachar Gal  wrote:
>>
>>> hello,
>>> I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version)
>>> on ubuntu, and I encounter this error (copying from the recon-all.log)
>>> ___
>>> #@# Talairach Sun Jan 13 17:35:07 IST 2019
>>> /home/shachar/piano_hcp/102/102/mri
>>>
>>>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>>> --i orig.mgz --o orig_nu.mgz
>>>
>>> Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC
>>> 2018 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019
>>> ___
>>>
>>> i'm a bit confused by the lack of error descriptions, and would
>>> appreciate any leads for solving it :)
>>>
>>> Shachar
>>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
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Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

thanks,
hope it'll work
anyway, looking forward for the version 6 release

cheers,
Shachar

On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew  wrote:

> Ubuntu 14.04 should still work.
>
> Matt.
>
> From: Shachar Gal 
> Date: Monday, January 14, 2019 at 5:43 AM
> To: Freesurfer support list , Matt
> Glasser , Ido Tavor 
> Subject: Re: problem using recon-all
>
> if the problem is with the versions, maybe downgrading my OS for now will
> do the trick? do you happen know what is the latest ubuntu that is
> compatible with the 5.3-HCP version?
> does this also occur in centOS?
>
> thanks
>
> On Sun, 13 Jan 2019 at 17:46 Shachar Gal  wrote:
>
>> hello,
>> I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on
>> ubuntu, and I encounter this error (copying from the recon-all.log)
>> ___
>> #@# Talairach Sun Jan 13 17:35:07 IST 2019
>> /home/shachar/piano_hcp/102/102/mri
>>
>>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>> --i orig.mgz --o orig_nu.mgz
>>
>> Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC
>> 2018 x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019
>> ___
>>
>> i'm a bit confused by the lack of error descriptions, and would
>> appreciate any leads for solving it :)
>>
>> Shachar
>>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
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Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

Ubuntu 14.04 should still work.

Matt.

From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, January 14, 2019 at 5:43 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>, Matt 
Glasser mailto:glass...@wustl.edu>>, Ido Tavor 
mailto:idota...@gmail.com>>
Subject: Re: problem using recon-all

if the problem is with the versions, maybe downgrading my OS for now will do 
the trick? do you happen know what is the latest ubuntu that is compatible with 
the 5.3-HCP version?
does this also occur in centOS?

thanks

On Sun, 13 Jan 2019 at 17:46 Shachar Gal 
mailto:gal.shac...@gmail.com>> wrote:
hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on 
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

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

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 
___

i'm a bit confused by the lack of error descriptions, and would appreciate any 
leads for solving it :)

Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

if the problem is with the versions, maybe downgrading my OS for now will
do the trick? do you happen know what is the latest ubuntu that is
compatible with the 5.3-HCP version?
does this also occur in centOS?

thanks

On Sun, 13 Jan 2019 at 17:46 Shachar Gal  wrote:

> hello,
> I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on
> ubuntu, and I encounter this error (copying from the recon-all.log)
> ___
> #@# Talairach Sun Jan 13 17:35:07 IST 2019
> /home/shachar/piano_hcp/102/102/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
> --i orig.mgz --o orig_nu.mgz
>
> Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019
> ___
>
> i'm a bit confused by the lack of error descriptions, and would appreciate
> any leads for solving it :)
>
> Shachar
>
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Re: [Freesurfer] problem using recon-all

[Glasser, Matthew]

External Email - Use Caution

This is a known issue with this version of FreeSurfer and newer Ubuntu OS.  We 
hope to have a version of the HCP Pipelines compatible with FreeSurfer 6.0+ in 
the coming weeks.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Sunday, January 13, 2019 at 9:46 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] problem using recon-all


External Email - Use Caution

hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on 
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

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

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 
___

i'm a bit confused by the lack of error descriptions, and would appreciate any 
leads for solving it :)

Shachar


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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[Freesurfer] problem using recon-all

[Shachar Gal]

External Email - Use Caution

hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

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

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019
___

i'm a bit confused by the lack of error descriptions, and would appreciate
any leads for solving it :)

Shachar
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Re: [Freesurfer] Problem with Recon-All for Volmetric

[Bruce Fischl]

you mean not to generate surfaces/parcellations/thickness? I guess you 
could run -autorecon1 -autorecon2. That would do the start of the surface 
stuff, but not much (and not long)


cheers
Bruce
On Tue, 30 May 2017, Becker, Valerie 
wrote:




Hi all,


Forgive me, as I' new at this, but I cant seem to quite make heads or tails
of the Recon-all page with instructions on how to divide it the commands.
We're just trying to run individual volumetric analyses at the moment. Is
there a way to do that with a recon- proc? So as to shorten processing time?


Thanks,

Valerie

UT Dallas


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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] Problem with Recon-All for Volmetric

[Douglas N Greve]

you can run it with -autorecon1 -autorecon2



On 05/30/2017 04:00 PM, Becker, Valerie wrote:
>
> Hi all,
>
>
> Forgive me, as I' new at this, but I cant seem to quite make heads or 
> tails of the Recon-all page with instructions on how to divide it the 
> commands. We're just trying to run individual volumetric analyses at 
> the moment. Is there a way to do that with a recon- proc? So as to 
> shorten processing time?
>
>
> Thanks,
>
> Valerie
>
> UT Dallas
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Problem with Recon-All for Volmetric

[Becker, Valerie]

Hi all,


Forgive me, as I' new at this, but I cant seem to quite make heads or tails of 
the Recon-all page with instructions on how to divide it the commands. We're 
just trying to run individual volumetric analyses at the moment. Is there a way 
to do that with a recon- proc? So as to shorten processing time?


Thanks,

Valerie

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

Re: [Freesurfer] Problem running recon-all in newly installed Ubuntu 16.04LTS

[Nasos Petridis]

Hi Bruce,

Many thanks. The PC has nominally 8Gb of RAM. The recon-all.log gives 
the following

 totalusedfree 
shared  buff/cache   available
Mem:8142944 1081848 6041324   44260 1019772 6725212
Swap:   8353788   0 8353788


Can the problem be that it's only 6.6Gb available?

Nikos

On 07/12/2016 16:32, Bruce Fischl wrote:
> Hi Nasos
>
> how much RAM is on your new PC?
>
> cheers
> Bruce
> On Wed, 7 Dec 2016, Nasos Petridis wrote:
>
>> Hello freesurfer experts,
>>
>> I've recently set up a PC running Ubuntu 16.04LTS and tried to run a
>> freesurfer version which was running well on another PC (also running
>> Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm
>> running the recon-all script. While running mri_ca_register, I get
>>
>> label assignment complete, 7 changed (0.00%)
>> det(m_affine) = 1.19 (predicted orig area = 6.7)
>> label assignment complete, 8 changed (0.00%)
>> Segmentation fault (core dumped)
>> ERROR: mri_ca_register with non-zero status 139
>> but continuing despite the error
>> and a little bit later the program exits.
>>
>> Comparing the recon-all.log files from the runs in the two PCs, they
>> appear identical until the above error appears, with the exception of
>> the  "main basin size", where the problematic PC gives a value which is
>> 3.5% of that in the "good" PC.
>>
>> Any idea what may be going wrong with the new PC?
>>
>> Many thanks,
>>
>> Nasos
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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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.
>
>

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Re: [Freesurfer] Problem running recon-all in newly installed Ubuntu 16.04LTS

[Bruce Fischl]

Hi Nasos

how much RAM is on your new PC?

cheers
Bruce
On Wed, 7 Dec 2016, Nasos Petridis wrote:

> Hello freesurfer experts,
>
> I've recently set up a PC running Ubuntu 16.04LTS and tried to run a
> freesurfer version which was running well on another PC (also running
> Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm
> running the recon-all script. While running mri_ca_register, I get
>
> >>
>
> label assignment complete, 7 changed (0.00%)
> det(m_affine) = 1.19 (predicted orig area = 6.7)
> label assignment complete, 8 changed (0.00%)
> Segmentation fault (core dumped)
> ERROR: mri_ca_register with non-zero status 139
> but continuing despite the error
> >>
>
> and a little bit later the program exits.
>
> Comparing the recon-all.log files from the runs in the two PCs, they
> appear identical until the above error appears, with the exception of
> the  "main basin size", where the problematic PC gives a value which is
> 3.5% of that in the "good" PC.
>
> Any idea what may be going wrong with the new PC?
>
> Many thanks,
>
> Nasos
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[Freesurfer] Problem running recon-all in newly installed Ubuntu 16.04LTS

[Nasos Petridis]

Hello freesurfer experts,

I've recently set up a PC running Ubuntu 16.04LTS and tried to run a 
freesurfer version which was running well on another PC (also running 
Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm 
running the recon-all script. While running mri_ca_register, I get

 >>

label assignment complete, 7 changed (0.00%)
det(m_affine) = 1.19 (predicted orig area = 6.7)
label assignment complete, 8 changed (0.00%)
Segmentation fault (core dumped)
ERROR: mri_ca_register with non-zero status 139
but continuing despite the error
 >>

and a little bit later the program exits.

Comparing the recon-all.log files from the runs in the two PCs, they 
appear identical until the above error appears, with the exception of 
the  "main basin size", where the problematic PC gives a value which is 
3.5% of that in the "good" PC.

Any idea what may be going wrong with the new PC?

Many thanks,

Nasos
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Re: [Freesurfer] Problem with recon-all

[Bruce Fischl]

Hi Mads

yes, you should be able to use mri_convert to change it to .mgz format 
and name it brainmask.mgz, after which I think it will look as if you've 
manually edited it and it will be applied

cheers
Bruce
On Mon, 12 Oct 2015, Mads Jensen 
wrote:

> I got a skullstrippen mask from another pipeline to remove the noise
> in the MP2RAGE. Is it possible to give that to the recon-all? it is
> either a mnc or nii
>
> thanks,
> mads
>
> On 5 October 2015 at 23:11, Andre van der Kouwe
>  wrote:
>> I think the standard MP2RAGE only generates the T1 image on the scanner.
>> With the Bloch simulation you can also figure out PD but the online
>> image analysis doesn't do it.
>>
>> On 10/05/2015 04:21 PM, Bruce Fischl wrote:
>>> I thought mp2rage lets you derive a proton-density (PD) weighted image,
>>> but I could be wrong. I'll cc Andre van der Kouwe who will know
>>>
>>>
>>> On Mon, 5 Oct 2015, Mads Jensen wrote:
>>>
 Hi and thanks for the fast reply.

 Pardon my ignorance, but I am not sure that the PD images are?

 thanks,
 mads

 On 5 October 2015 at 21:59, Bruce Fischl 
 wrote:
> Hi Mads
>
> my guess is that this is a problem with the MP2RAGE. We don't see
> this in
> the mprage or memprage. Can you look at the PD images in that region? Is
> the PD close to 0? Maybe you can threshold it out? That region is
> usually
> very dark on an mprage
>
> cheers
> Bruce
>
>
> On Mon, 5 Oct 2015, Mads Jensen wrote:
>
>> Hi,
>>
>> I got a problem with recon-all of T1's. The problem is that the
>> surfaces extent into what is essential noise, see linked images. The
>> problem is reoccurring in all the subjects I have ran so far, so I was
>> wondering if there could be a generic fix or if it will be necessary
>> to fix each recon individually.
>>
>> The sequence is a MP2RAGE recorded from a Siemens Skyra.
>>
>> thanks,
>> mads
>>
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg
>>
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg
>>
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg
>>
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg
>>
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg
>>
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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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
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>>>
>>>
>> ___
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Re: [Freesurfer] Problem with recon-all

[Mads Jensen]

I got a skullstrippen mask from another pipeline to remove the noise
in the MP2RAGE. Is it possible to give that to the recon-all? it is
either a mnc or nii

thanks,
mads

On 5 October 2015 at 23:11, Andre van der Kouwe
 wrote:
> I think the standard MP2RAGE only generates the T1 image on the scanner.
> With the Bloch simulation you can also figure out PD but the online
> image analysis doesn't do it.
>
> On 10/05/2015 04:21 PM, Bruce Fischl wrote:
>> I thought mp2rage lets you derive a proton-density (PD) weighted image,
>> but I could be wrong. I'll cc Andre van der Kouwe who will know
>>
>>
>> On Mon, 5 Oct 2015, Mads Jensen wrote:
>>
>>> Hi and thanks for the fast reply.
>>>
>>> Pardon my ignorance, but I am not sure that the PD images are?
>>>
>>> thanks,
>>> mads
>>>
>>> On 5 October 2015 at 21:59, Bruce Fischl 
>>> wrote:
 Hi Mads

 my guess is that this is a problem with the MP2RAGE. We don't see
 this in
 the mprage or memprage. Can you look at the PD images in that region? Is
 the PD close to 0? Maybe you can threshold it out? That region is
 usually
 very dark on an mprage

 cheers
 Bruce


 On Mon, 5 Oct 2015, Mads Jensen wrote:

> Hi,
>
> I got a problem with recon-all of T1's. The problem is that the
> surfaces extent into what is essential noise, see linked images. The
> problem is reoccurring in all the subjects I have ran so far, so I was
> wondering if there could be a generic fix or if it will be necessary
> to fix each recon individually.
>
> The sequence is a MP2RAGE recorded from a Siemens Skyra.
>
> thanks,
> mads
>
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg
>
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg
>
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg
>
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg
>
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg
>
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>>
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Re: [Freesurfer] Problem with recon-all

[Mads Jensen]

Hi and thanks for the fast reply.

Pardon my ignorance, but I am not sure that the PD images are?

thanks,
mads

On 5 October 2015 at 21:59, Bruce Fischl  wrote:
> Hi Mads
>
> my guess is that this is a problem with the MP2RAGE. We don't see this in
> the mprage or memprage. Can you look at the PD images in that region? Is
> the PD close to 0? Maybe you can threshold it out? That region is usually
> very dark on an mprage
>
> cheers
> Bruce
>
>
> On Mon, 5 Oct 2015, Mads Jensen wrote:
>
>> Hi,
>>
>> I got a problem with recon-all of T1's. The problem is that the
>> surfaces extent into what is essential noise, see linked images. The
>> problem is reoccurring in all the subjects I have ran so far, so I was
>> wondering if there could be a generic fix or if it will be necessary
>> to fix each recon individually.
>>
>> The sequence is a MP2RAGE recorded from a Siemens Skyra.
>>
>> thanks,
>> mads
>>
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg
>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
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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.
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Re: [Freesurfer] Problem with recon-all

[Bruce Fischl]

Hi Mads

my guess is that this is a problem with the MP2RAGE. We don't see this in 
the mprage or memprage. Can you look at the PD images in that region? Is 
the PD close to 0? Maybe you can threshold it out? That region is usually 
very dark on an mprage

cheers
Bruce


On Mon, 5 Oct 2015, Mads Jensen wrote:

> Hi,
>
> I got a problem with recon-all of T1's. The problem is that the
> surfaces extent into what is essential noise, see linked images. The
> problem is reoccurring in all the subjects I have ran so far, so I was
> wondering if there could be a generic fix or if it will be necessary
> to fix each recon individually.
>
> The sequence is a MP2RAGE recorded from a Siemens Skyra.
>
> thanks,
> mads
>
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg
> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Problem with recon-all

[Andre van der Kouwe]

I think the standard MP2RAGE only generates the T1 image on the scanner. 
With the Bloch simulation you can also figure out PD but the online 
image analysis doesn't do it.

On 10/05/2015 04:21 PM, Bruce Fischl wrote:
> I thought mp2rage lets you derive a proton-density (PD) weighted image,
> but I could be wrong. I'll cc Andre van der Kouwe who will know
>
>
> On Mon, 5 Oct 2015, Mads Jensen wrote:
>
>> Hi and thanks for the fast reply.
>>
>> Pardon my ignorance, but I am not sure that the PD images are?
>>
>> thanks,
>> mads
>>
>> On 5 October 2015 at 21:59, Bruce Fischl 
>> wrote:
>>> Hi Mads
>>>
>>> my guess is that this is a problem with the MP2RAGE. We don't see
>>> this in
>>> the mprage or memprage. Can you look at the PD images in that region? Is
>>> the PD close to 0? Maybe you can threshold it out? That region is
>>> usually
>>> very dark on an mprage
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 5 Oct 2015, Mads Jensen wrote:
>>>
 Hi,

 I got a problem with recon-all of T1's. The problem is that the
 surfaces extent into what is essential noise, see linked images. The
 problem is reoccurring in all the subjects I have ran so far, so I was
 wondering if there could be a generic fix or if it will be necessary
 to fix each recon individually.

 The sequence is a MP2RAGE recorded from a Siemens Skyra.

 thanks,
 mads

 https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg

 https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg

 https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg

 https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg

 https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg

 https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg

 ___
 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.
>>>
>> ___
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[Freesurfer] Problem with recon-all

[Mads Jensen]

Hi,

I got a problem with recon-all of T1's. The problem is that the
surfaces extent into what is essential noise, see linked images. The
problem is reoccurring in all the subjects I have ran so far, so I was
wondering if there could be a generic fix or if it will be necessary
to fix each recon individually.

The sequence is a MP2RAGE recorded from a Siemens Skyra.

thanks,
mads

https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg
https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg
https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg
https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg
https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg
https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Problem with recon-all

[Bruce Fischl]

I thought mp2rage lets you derive a proton-density (PD) weighted image, but 
I could be wrong. I'll cc Andre van der Kouwe who will know


On Mon, 5 Oct 2015, Mads Jensen wrote:

> Hi and thanks for the fast reply.
>
> Pardon my ignorance, but I am not sure that the PD images are?
>
> thanks,
> mads
>
> On 5 October 2015 at 21:59, Bruce Fischl  wrote:
>> Hi Mads
>>
>> my guess is that this is a problem with the MP2RAGE. We don't see this in
>> the mprage or memprage. Can you look at the PD images in that region? Is
>> the PD close to 0? Maybe you can threshold it out? That region is usually
>> very dark on an mprage
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 5 Oct 2015, Mads Jensen wrote:
>>
>>> Hi,
>>>
>>> I got a problem with recon-all of T1's. The problem is that the
>>> surfaces extent into what is essential noise, see linked images. The
>>> problem is reoccurring in all the subjects I have ran so far, so I was
>>> wondering if there could be a generic fix or if it will be necessary
>>> to fix each recon individually.
>>>
>>> The sequence is a MP2RAGE recorded from a Siemens Skyra.
>>>
>>> thanks,
>>> mads
>>>
>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg
>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.jpg
>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg
>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.jpg
>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg
>>> https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.jpg
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
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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.
>>
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[Freesurfer] Problem with recon-all

[Andrea Tateo]

Dear FS experts,
I have a problem with the command recon-all.

In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING 
INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are 
killed at the command nu_currect, as you can see from the file.log in 
attachment.
Do you have any suggestions?

Thanks a lot for your help.

Best regardes,

Andrea

   Thu May 23 13:58:52 CEST 2013
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001
/opt/exp_soft/mag/freesurfer/bin/recon-all
-debug -s 001 -autorecon-all
subjid 001
setenv SUBJECTS_DIR /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16
FREESURFER_HOME /opt/exp_soft/mag/freesurfer
Actual FREESURFER_HOME /opt/exp_soft/mag/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux pccms114.ba.infn.it 2.6.18-348.1.1.el5 #1 SMP Thu Jan 24 13:25:42 CET 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  32768 
memorylocked 32 kbytes
maxproc  386293 

 total   used   free sharedbuffers cached
Mem:  49448428   462321603216268  0 900488   29561664
-/+ buffers/cache:   15770008   33678420
Swap: 16779884 613964   16165920


program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:53-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:53-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:53-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:53-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:53-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:54-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:54-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:54-GMT  BuildTimeStamp: May 22 2011 08:23:31  CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $  User: tateo  Machine: pccms114.ba.infn.it  Platform: Linux  PlatformVersion: 2.6.18-348.1.1.el5  CompilerName: GCC  CompilerVersion: 30400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/05/23-11:58:54-GMT  BuildTimeStamp: May 22 

Re: [Freesurfer] Problem running recon-all with option -qcache

[Ed Gronenschild]

Hi Doug,

Indeed, you are right, I forgot to run recon-all -autorecon3.

It is not well documented that after running -autorecon2-wm
one should also run -autorecon3. I had the impression that
this portion was executed automatically by -autorecon2-wm.

Ed

On 2 Feb 2011, at 18:03, Douglas N Greve wrote:

 Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll  
 need
 to re-run some portion of recon-all depending upon where in the stream
 it aborted.

 doug

 Ed Gronenschild wrote:
 Hi,

 A serious error was encountered in running recon-all with option
 -qcache.
 The error occurred during execution of mri_surf2surf and the
 message was:

 number of vertices in ../subjectID/surf/lh.thickness does not  
 match
 surface (141969,131763).

 It means the number of vertices in lh.sphere.reg does not
 match the number in lh.thickness.

 I traced the course of this error and that is causing me serious
 troubles. What happened? I edited the wm voxels and then
 invoked another call to recon-all by issueing the command
 recon-all -autorecon2-wm.
 Looking at the dates of the files in the surf directory I noticed
 that the file lh.sphere.reg was not updated, so it was still the
 same file as before editing the wm voxels. The lh.thickness
 was correctly updated as expected.

 What can I do to use the -qcache option?

 Ed

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




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

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



 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] Problem running recon-all with option -qcache

[Douglas N Greve]

Thanks for the suggestion Ed. I've just added the text below to 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Troubleshooting. If 
you know of another place where it would be useful, please let us know.

doug

Note that after you run recon-all with the -autorecon2-wm flag, you 
will still need to run it with the -autorecon3 flag. You can run it with 
both -autorecon2-wm and -autorecon3, though if the changes you made did 
not fix the problem, then the time spent running autorecon3 will be wasted.

Ed Gronenschild wrote:
 Hi Doug,

 Indeed, you are right, I forgot to run recon-all -autorecon3.

 It is not well documented that after running -autorecon2-wm
 one should also run -autorecon3. I had the impression that
 this portion was executed automatically by -autorecon2-wm.

 Ed

 On 2 Feb 2011, at 18:03, Douglas N Greve wrote:

   
 Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll  
 need
 to re-run some portion of recon-all depending upon where in the stream
 it aborted.

 doug

 Ed Gronenschild wrote:
 
 Hi,

 A serious error was encountered in running recon-all with option
 -qcache.
 The error occurred during execution of mri_surf2surf and the
 message was:

 number of vertices in ../subjectID/surf/lh.thickness does not  
 match
 surface (141969,131763).

 It means the number of vertices in lh.sphere.reg does not
 match the number in lh.thickness.

 I traced the course of this error and that is causing me serious
 troubles. What happened? I edited the wm voxels and then
 invoked another call to recon-all by issueing the command
 recon-all -autorecon2-wm.
 Looking at the dates of the files in the surf directory I noticed
 that the file lh.sphere.reg was not updated, so it was still the
 same file as before editing the wm voxels. The lh.thickness
 was correctly updated as expected.

 What can I do to use the -qcache option?

 Ed

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



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

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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

 

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


   

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] Problem running recon-all with option -qcache

[Ed Gronenschild]

Hi,

A serious error was encountered in running recon-all with option
-qcache.
The error occurred during execution of mri_surf2surf and the
message was:

number of vertices in ../subjectID/surf/lh.thickness does not match
surface (141969,131763).

It means the number of vertices in lh.sphere.reg does not
match the number in lh.thickness.

I traced the course of this error and that is causing me serious
troubles. What happened? I edited the wm voxels and then
invoked another call to recon-all by issueing the command
recon-all -autorecon2-wm.
Looking at the dates of the files in the surf directory I noticed
that the file lh.sphere.reg was not updated, so it was still the
same file as before editing the wm voxels. The lh.thickness
was correctly updated as expected.

What can I do to use the -qcache option?

Ed

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

Re: [Freesurfer] Problem running recon-all with option -qcache

[Douglas N Greve]

Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need 
to re-run some portion of recon-all depending upon where in the stream 
it aborted.

doug

Ed Gronenschild wrote:
 Hi,

 A serious error was encountered in running recon-all with option
 -qcache.
 The error occurred during execution of mri_surf2surf and the
 message was:

 number of vertices in ../subjectID/surf/lh.thickness does not match
 surface (141969,131763).

 It means the number of vertices in lh.sphere.reg does not
 match the number in lh.thickness.

 I traced the course of this error and that is causing me serious
 troubles. What happened? I edited the wm voxels and then
 invoked another call to recon-all by issueing the command
 recon-all -autorecon2-wm.
 Looking at the dates of the files in the surf directory I noticed
 that the file lh.sphere.reg was not updated, so it was still the
 same file as before editing the wm voxels. The lh.thickness
 was correctly updated as expected.

 What can I do to use the -qcache option?

 Ed

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


   

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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

Re: [Freesurfer] problem on recon-all

[Allison Stevens]

Xiaoying,
There are directions for how to do this located here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ?highlight=%28FAQ%29#SkullStrippingOptions
Allison

-- 

On Fri, 12 Mar 2010, Xiaoying Tang wrote:

 Hi all,

 When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in 
 sequence. But now suppose I have already have a very good skull-stripped 
 subject. I mean I don't need to do skull-stripping with freesurfer. But I 
 want to get greymatter and white matter, which are generated in autorecon2 
 and autorecon3. Is there any way to do this?

 Looking forward to your early reply.

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



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

Re: [Freesurfer] problem on recon-all

[Xiaoying Tang]

Hi Allison,

You are so helpful. Thanks a lot.

Best,
Xiaoying

- Original Message -
From: Allison Stevens astev...@nmr.mgh.harvard.edu
Date: Friday, March 12, 2010 7:43 am
Subject: Re: [Freesurfer] problem on recon-all
To: Xiaoying Tang xta...@jhu.edu
Cc: freesurfer@nmr.mgh.harvard.edu


 Xiaoying,
 There are directions for how to do this located here:
 
 Allison
 
 -- 
 
 On Fri, 12 Mar 2010, Xiaoying Tang wrote:
 
  Hi all,
 
  When we do recon-all, we usually do autorecon1, autorecon2, and 
 autorecon3 in sequence. But now suppose I have already have a very 
 good skull-stripped subject. I mean I don't need to do skull-stripping 
 with freesurfer. But I want to get greymatter and white matter, which 
 are generated in autorecon2 and autorecon3. Is there any way to do this?
 
  Looking forward to your early reply.
 
  Best,
  Xiaoying
  ___
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  Freesurfer@nmr.mgh.harvard.edu
  
 
 
 
 
 
 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
  . If the e-mail was sent to you in error
 but does not contain patient information, please contact the sender 
 and properly
 dispose of the e-mail.
 
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] problem on recon-all

[Xiaoying Tang]

Hi all,

When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in 
sequence. But now suppose I have already have a very good skull-stripped 
subject. I mean I don't need to do skull-stripping with freesurfer. But I want 
to get greymatter and white matter, which are generated in autorecon2 and 
autorecon3. Is there any way to do this?

Looking forward to your early reply.

Best,
Xiaoying
___
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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] Problem with recon-all on the tutorial data (bert)

[Long]

Dear Bruce,
I have tried running mri_ca_register again twice with the following cases:
 Case 1: on VirtualBox with 9.2GB available free disk space. I gave 1GB
RAM to this Virtual Machine.
 Case 2: on Ubuntu installed on a machine with 2 core Dual 2.5Ghz , 4G
RAM, and 6GB free disk space.
In both cases, I have got the same result as described in the previous mail:
segmentation fault.
Would you have any suggestion for this problem?
Thank you.
Bests,
Long


On Tue, Nov 24, 2009 at 9:05 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Long,

 have you run out of disk space?
 Bruce

 On Tue, 24 Nov 2009, L wrote:

  Dear Freesurfers,

 I have had a problem when running recon-all on your tutorial data (bert).
 Please find following the content of recon-all.log:

 *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $*

 *  $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $*

 *MRISread(../surf/lh.inflated): could not open file*

 *No such file or directory*

 *mris_sphere: could not read surface file ../surf/lh.inflated*

 *No such file or directory*

 *Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
 01:57:59 UTC 2009 i686 GNU/Linux*

 * *

 *recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009*



 I suspected that the problem occurred at ?mri_ca_register? and reran it as
 following:

 *mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T
 transforms/talairach.lta norm.mgz
 $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z*

 * *

 It said the following at the end of the process and ?talairach.m3z? could
 not be found in dir ?transforms/?

 *?*

 *0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625*

 *0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625*

 *0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625*
 **

 *writing output transformation to transforms/talairach.m3z...*

 *Segmentation fault*

 * *

 Here is what given by ?bugr? command:

 *FREESURFER_HOME: /usr/local/freesurfer*

 *Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0*

 *Debian version: 5.0  *

 *Kernel info: Linux 2.6.28-11-generic i686*



 I am running the VirtualBox Ubuntu version.

 I have looked at previous posts but have not been able to figure out an
 appropriate answer to my problem. Any of your help would be highly
 appreciated.

 Thank you.

 Kind regards,

 Long


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[Freesurfer] Problem with recon-all on the tutorial data (bert)

[L]

Dear Freesurfers,

I have had a problem when running recon-all on your tutorial data (bert).
Please find following the content of recon-all.log:

*$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $*

*  $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $*

*MRISread(../surf/lh.inflated): could not open file*

*No such file or directory*

*mris_sphere: could not read surface file ../surf/lh.inflated*

*No such file or directory*

*Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
01:57:59 UTC 2009 i686 GNU/Linux*

* *

*recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009*



I suspected that the problem occurred at “mri_ca_register” and reran it as
following:

*mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T
transforms/talairach.lta norm.mgz
$FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z*

* *

It said the following at the end of the process and “talairach.m3z” could
not be found in dir “transforms/”

*…*

*0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625*

*0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625*

*0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625*
**

*writing output transformation to transforms/talairach.m3z...*

*Segmentation fault*

* *

Here is what given by “bugr” command:

*FREESURFER_HOME: /usr/local/freesurfer*

*Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0*

*Debian version: 5.0  *

*Kernel info: Linux 2.6.28-11-generic i686*



I am running the VirtualBox Ubuntu version.

I have looked at previous posts but have not been able to figure out an
appropriate answer to my problem. Any of your help would be highly
appreciated.

Thank you.

Kind regards,

Long
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Re: [Freesurfer] Problem with recon-all on the tutorial data (bert)

[Bruce Fischl]

Hi Long,

have you run out of disk space?
Bruce
On Tue, 24 Nov 2009, L wrote:

 Dear Freesurfers,

 I have had a problem when running recon-all on your tutorial data (bert).
 Please find following the content of recon-all.log:

 *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $*

 *  $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $*

 *MRISread(../surf/lh.inflated): could not open file*

 *No such file or directory*

 *mris_sphere: could not read surface file ../surf/lh.inflated*

 *No such file or directory*

 *Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
 01:57:59 UTC 2009 i686 GNU/Linux*

 * *

 *recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009*



 I suspected that the problem occurred at ?mri_ca_register? and reran it as
 following:

 *mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T
 transforms/talairach.lta norm.mgz
 $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z*

 * *

 It said the following at the end of the process and ?talairach.m3z? could
 not be found in dir ?transforms/?

 *?*

 *0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625*

 *0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625*

 *0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625*
 **

 *writing output transformation to transforms/talairach.m3z...*

 *Segmentation fault*

 * *

 Here is what given by ?bugr? command:

 *FREESURFER_HOME: /usr/local/freesurfer*

 *Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0*

 *Debian version: 5.0  *

 *Kernel info: Linux 2.6.28-11-generic i686*



 I am running the VirtualBox Ubuntu version.

 I have looked at previous posts but have not been able to figure out an
 appropriate answer to my problem. Any of your help would be highly
 appreciated.

 Thank you.

 Kind regards,

 Long

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[Freesurfer] problem with recon-all

[Russ Poldrack]

hi folks - I'm trying to get freesurfer (the latest Tiger snapshot) working on my mac but I'm having a problem with recon-all.  If I try to apply it to the bert data included in the distribution, it seems to set up ok but then it doesn't actually do anything.  here is the output from "recon-all-nmr -all -subjid bert" (same thing happens if I just use recon-all):Fri Jul 22 13:33:27 PDT 2005/Users/Shared/freesurfer/bin//recon-all-nmr-all -subjid bert/Users/Shared/freesurfer/subjects/bertsubjid bertSUBJECTS_DIR /Users/Shared/freesurfer/subjectsFREESURFER_HOME /Users/Shared/freesurferAutoSeg Enable =  1Darwinprogram versions used$Id: recon-all-nmr,v 1.71 2005/07/11 22:46:53 greve Exp $$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $mri_convert --version$$Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $minctracc.c$Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $!p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $$Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $$Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $mri_convert --version$# $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $#  $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $###Using COR formathere it just stops, which is presumably not the expected behavior with the -all flag.  I also tried with a new dataset converted to mgz format and with the -autorecon1 option and the same thing happens.  Any ideas what might be going on here?cheersruss ---  Russell A. Poldrack, Ph.d.  Assistant Professor  UCLA Department of Psychology  Franz  Hall, Box 951563  Los Angeles, CA 90095-1563   phone: 310-794-1224  fax: 310-206-5895  email: [EMAIL PROTECTED]  web: www.poldracklab.org   ___
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[Freesurfer] problem with recon-all

[Tamara Knutsen]

when i source: 
Setting up environment for FreeSurfer/FS-FAST
FREESURFER_HOME /usr/local/freesurfer/dev
FSFAST_HOME /usr/local/freesurfer/dev/fsfast
SUBJECTS_DIR/space/sake/3/users/inverse/subjects
FUNCTIONALS_DIR /usr/local/freesurfer/dev/sessions
MINC_BIN_DIR/usr/pubsw/packages/mni/current/bin
MINC_LIB_DIR/usr/pubsw/packages/mni/current/lib
FSL_DIR /usr/pubsw/packages/fsl/current
QTDIR   /usr/lib/qt3-gcc2.96

setenv SUBJECTS_DIR /space/orsay/2/knutsen

and then run:
recon-all-nmr -subjid ben -stage4b

i get this error:
[whatever:knutsen] (nmr-dev-env) recon-all-nmr -subjid jerry -stage4b
INFO: SUBJECTS_DIR is /autofs/space/orsay_002/knutsen

program versions used
$Id: recon-all-nmr,v 1.68 2005/07/07 04:59:34 greve Exp $
$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
mri_convert --version 
 $
$Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 
6.3 1999/10/19 14:45:31 neelin Exp $
minctracc.c
$Header: 
/software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 
96.3 2000/03/15 08:42:41 stever Exp $
$Header: 
/software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 
1999/10/19 14:45:27 neelin Exp $
$Header: 
/software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 
1999/10/19 14:45:18 neelin Exp $
$Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $
mri_convert --version 
 $
# $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $
#  $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
 $
###
ERROR: cannot determine format of input

When Leeland runs the same thing from his computer, it runs fine.

What is wrong with my setup that I cannot run this?

Thanks,
Tamara

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Re: [Freesurfer] problem with recon-all

[Doug Greve]

I modified recon-all to try to autodetect the input format (but 
introduced a bug). It should work if you add -COR to the command-line. 
In the mean time I'll fix my mistake.


doug




Tamara Knutsen wrote:

when i source: 
Setting up environment for FreeSurfer/FS-FAST

FREESURFER_HOME /usr/local/freesurfer/dev
FSFAST_HOME /usr/local/freesurfer/dev/fsfast
SUBJECTS_DIR/space/sake/3/users/inverse/subjects
FUNCTIONALS_DIR /usr/local/freesurfer/dev/sessions
MINC_BIN_DIR/usr/pubsw/packages/mni/current/bin
MINC_LIB_DIR/usr/pubsw/packages/mni/current/lib
FSL_DIR /usr/pubsw/packages/fsl/current
QTDIR   /usr/lib/qt3-gcc2.96

setenv SUBJECTS_DIR /space/orsay/2/knutsen

and then run:
recon-all-nmr -subjid ben -stage4b

i get this error:
[whatever:knutsen] (nmr-dev-env) recon-all-nmr -subjid jerry -stage4b
INFO: SUBJECTS_DIR is /autofs/space/orsay_002/knutsen

program versions used
$Id: recon-all-nmr,v 1.68 2005/07/07 04:59:34 greve Exp $
$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
mri_convert --version 
$
$Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 
6.3 1999/10/19 14:45:31 neelin Exp $

minctracc.c
$Header: 
/software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 
96.3 2000/03/15 08:42:41 stever Exp $
$Header: 
/software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 
1999/10/19 14:45:27 neelin Exp $
$Header: 
/software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 
1999/10/19 14:45:18 neelin Exp $

$Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $
mri_convert --version 
$

# $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $
#  $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
$
###
ERROR: cannot determine format of input

When Leeland runs the same thing from his computer, it runs fine.

What is wrong with my setup that I cannot run this?

Thanks,
Tamara

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


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[Freesurfer] Problem running recon-all

[Damaraju, Eswar]

Hello everyone,

I have recently upgraded my OS from RedHat Linux 9 to RedHat Enterprise 
edition. After that, I'm 
getting the following error when I run : $ recon-all -sid  -stage1


###
INFO: SUBJECTS_DIR is /home/edamaraju/freesurfer/subjects
-
MotionCor Tue Dec 21 18:22:55 EST 2004

INFO: no runs were found in 
/home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig/XXX,
however, there is a volume in 
/home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig,
so I am just going to proceed with that as the input.
-
Talairach Tue Dec 21 18:22:57 EST 2004
/home/edamaraju/freesurfer/subjects/eFMRI02/mri
talairach2 eFMRI02
INFO: registering eFMRI02
Tue Dec 21 18:22:57 EST 2004

mri_convert orig orig/orig.mnc
mri_convert orig orig/orig.mnc
reading from orig...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to orig/orig.mnc...

mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc 
transforms/talairach.xfm

mri_add_xform_to_header 
/home/edamaraju/freesurfer/subjects/eFMRI02/mri/transforms/talairach.xfm 
/home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig 
/home/edamaraju/freesurfer/subjects/eFMRI02/mri/orig
Tue Dec 21 18:24:00 EST 2004
-
Nu Intensity Correction Tue Dec 21 18:24:00 EST 2004
mri_convert orig nu/nu0.mnc
mri_convert orig nu/nu0.mnc
reading from orig...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to nu/nu0.mnc...
nu_correct -clobber nu/nu0.mnc nu/nu1.mnc
[EMAIL PROTECTED]:/home/edamaraju/freesurfer/subjects/eFMRI02/mri/] [2004-12-21 
18:24:09] running:
  /usr/pubsw04/packages04/mni/current/bin/nu_estimate_np_and_em -parzen -log 
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify 
-b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir 
/usr/tmp/nu_correct_13858/ nu/nu0.mnc nu/nu1.imp

/usr/pubsw04/packages04/mni/current/bin/volume_stats: error while loading 
shared libraries: libstdc++-libc6.1-1.so.2: cannot open shared object file: No 
such file or directory
nu_estimate_np_and_em: crashed while running volume_stats (termination 
status=32512)
nu_correct: crashed while running nu_estimate_np_and_em (termination 
status=32512)
ERROR: nu_correct



Where do I find these shared libraries? How should I link them?

Any help is appreciated.

Thanks,
Eswar.
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