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