Re: [Freesurfer] recon-all exited with error

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

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

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

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

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

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

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

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

best Trisanna

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

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

On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

you can put it on our ftp site:

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

...

Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a

place I can upload it to?

...

best Trisanna

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

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

fischl@nmr.mgh.harvard.edu> wrote:

...

  hmmm, I've never seen label2label core dump before. Can you tar,

gzip and

...

  upload the entire subject dir?
  On Tue, 16 Jan 2018, Trisanna Sprung-Much
  wrote:

  > Hi there
  >
  > I ran Freesurfer 6.0 on a subject last night and it took about

12 hours (seemed to get

...

  to the very end) and then exited with
  > errors. I can open my surfaces so I think it ended roughly with

the atlas labelling. I

...

  attach the recon-all log file here.
  >
  > best wishes
  >
  > Trisanna
  > --
  > Ph.D. CandidateMcGill University
  > Integrated Program in Neuroscience
  > Psychology
  >
  >
  >
  >
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