You can send it to either my email (ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>) or Bruce’s
best, Andrew On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: thanks Andrew. I had seen that and will give it a go - just wanted to make sure that my recipient email would be the FreeSurfer support list. Trisanna On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote: Hi Trisanna, Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange). best Andrew On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: Hi Andrew Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/> Connected to surfer.nmr.mgh.harvard.edu<http://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<http://surfer.nmr.mgh.harvard.edu/>:trisanna): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> quote PASV 227 Entering Passive Mode (132,183,202,158,147,251). ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. On Wed, Jan 17, 2018 at 5:59 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>> wrote: Hi Trisanna, Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue. best, Andrew On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: Sorry, Bruce. ignore my last email. Not sure what happened there. I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be? trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ls fsaverage icbm-109 icbm-118 icbm-127 icbm-142 icbm-202 icbm-102 icbm-110 icbm-119 icbm-131 icbm-143 icbm-202.tar.gz icbm-103 icbm-111 icbm-120 icbm-133 icbm-144 icbm-203 icbm-104 icbm-112 icbm-121 icbm-135 icbm-146 icbm-204 icbm-105 icbm-113 icbm-122 icbm-137 icbm-150 icbm-205 icbm-106 icbm-114 icbm-123 icbm-139 icbm-158 icbm-205.tar.gz icbm-107 icbm-115 icbm-125 icbm-140 icbm-200 icbm-206 icbm-108 icbm-117 icbm-126 icbm-141 icbm-201 trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp [X] surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/> Connected to [X] surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/>. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-[X]http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu<http://surfer.nmr.mgh.harvard.edu/>:trisanna): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> put icbm-205.tar.gz local: icbm-205.tar.gz remote: icbm-205.tar.gz 200 PORT command successful. Consider using PASV. 425 Failed to establish connection. -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jan 17, 2018 at 2:01 PM, Trisanna Sprung-Much <trisanna.sprung-m...@mail.mcgill.ca<mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further. To clarify, subjects 205 and now subject 202 have both failed after surface extraction. best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Jan 16, 2018 at 3:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@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 > <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote: > hmmm, I've never seen label2label core dump before. Can you tar, gzip > and > upload the entire subject dir? > On Tue, 16 Jan 2018, Trisanna Sprung-Much > wrote: > > > Hi there > > > > I ran Freesurfer 6.0 on a subject last night and it took about 12 > hours (seemed to get > to the very end) and then exited with > > errors. I can open my surfaces so I think it ended roughly with the > atlas labelling. I > attach the recon-all log file here. > > > > best wishes > > > > Trisanna > > -- > > Ph.D. CandidateMcGill University > > Integrated Program in Neuroscience > > Psychology > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > [X] [X] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > [X] [X] http://www.partners.org/complianceline . If the e-mail was sent > to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> [X][X]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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