best
Andrew
On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much <trisanna.sprung-much@mail.mcgill.ca> wrote:
_______________________________________________
Hi AndrewThank 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/compute r/nmr-aup.php
220-
220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220- and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220- try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
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 <AHOOPES@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-much@mail.mcgill.ca > wrote:
https://mail.nmr.mgh.harvard.e______________________________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 tosurfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard
.edu/martinos/userInfo/compute r/nmr-aup.php
220-
220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220- and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220- try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:trisanna): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
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. CandidateMcGill University
Integrated Program in NeurosciencePsychology
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.
bestTrisanna
--Ph.D. CandidateMcGill University
Integrated Program in NeurosciencePsychology
--Ph.D. CandidateMcGill University
Integrated Program in NeurosciencePsychology
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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