yn-128-59-230-36:structural michellevantieghem2$ 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:michellevantieghem2): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/outgoing 250 Directory successfully changed. ftp> put SB152_freesurfer.tar.gz local: SB152_freesurfer.tar.gz remote: SB152_freesurfer.tar.gz 229 Entering Extended Passive Mode (|||37860|). 553 Could not create file. ftp> ls 229 Entering Extended Passive Mode (|||37896|). 150 Here comes the directory listing. -rw-r--r-- 1 0 0 3812 Dec 01 06:10 README.1st drwxrwsr-t 4 0 1046 4096 Nov 21 2014 flat drwxrwsr-t 13 0 160 4096 Aug 19 2013 fsdev drwxrwsr-t 14 0 1046 4096 Dec 05 2011 recon drwxrwsr-t 3 0 18 4096 Jan 24 2005 sysadm 226 Directory send OK. ftp> ls 229 Entering Extended Passive Mode (|||37892|). 150 Here comes the directory listing. -rw-r--r-- 1 0 0 3812 Dec 01 06:10 README.1st drwxrwsr-t 4 0 1046 4096 Nov 21 2014 flat drwxrwsr-t 13 0 160 4096 Aug 19 2013 fsdev drwxrwsr-t 14 0 1046 4096 Dec 05 2011 recon drwxrwsr-t 3 0 18 4096 Jan 24 2005 sysadm 226 Directory send OK. ftp> put SB152_freesurfer.tar.gz local: SB152_freesurfer.tar.gz remote: SB152_freesurfer.tar.gz 229 Entering Extended Passive Mode (|||37898|). 553 Could not create file. ftp> On Fri, Dec 1, 2017 at 4:50 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > can you paste the full session text into the email (not as a screen shot)? > > > On Fri, 1 Dec 2017, Michelle VanTieghem wrote: > > Hi, I am unsure whether this worked: see attached screenshot. >> >> Thanks! >> M >> >> On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> yes, it should. You should just be able to do a "put" >> On Fri, 1 Dec 2017, Michelle VanTieghem wrote: >> >> Hi, >> I am confused by the instructions for the ftp. Once I am >> logged into the ftp and have navigated to >> the transfer/incoming >> directory, how am I supposed to find / access the file that I >> would ike to send through? Does >> terminal still recognize my >> working directory before I logged into the ftp? >> >> Thanks! >> Michelle >> >> On Sat, Nov 18, 2017 at 2:54 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> Hi Michelle >> >> probably best to tar and gzip the entire subject >> directory and ftp it to us: >> >> https://surfer.nmr.mgh.harvard >> .edu/fswiki/FtpFileExchange >> >> cheers >> Bruce >> >> On Sat, 18 Nov 2017, Michelle VanTieghem wrote: >> >> Hi, >> Yes I can send you the data - should I just >> attach the mprage file in the email, or is >> there >> another >> way to share the data with freesurfer? Also, >> should I send one scan or multiple >> scans? >> >> Thanks, >> Michelle >> >> On Sat, Nov 18, 2017 at 10:37 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> Hi Michelle >> >> are you doing anything out of the ordinary? >> Do you want to send us a dataset and >> we will >> take a look? I don't think 6.0 is very >> different from 5.3 in regard to skull >> stripping, >> although it is probably a bit better >> >> Bruce >> >> On Fri, 17 Nov 2017, Michelle VanTieghem >> wrote: >> >> Hello, >> I have posted several times about >> problems with skull-stripping with our >> dataset. We have tried gcut >> and multiple other options in other >> packages (AFNI, FSL, ANTS) to remove >> skull from structural >> images in our dataset with little >> success. >> >> Recently, a colleague suggested this >> may be due to versions: that 6.0 >> deals >> with skull stripping >> much better than 5.3. >> >> I wanted to ask if indeed this could >> be the case before I go install 6.0 >> and re-run everything in >> my study. >> >> Thank you, >> Michelle >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience >> Lab >> Columbia University >> mrv2...@columbia.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 >> 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. >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2...@columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2...@columbia.edu >> >> >> >> >> -- >> Michelle VanTieghem >> PhD student in Psychology >> Developmental Affective Neuroscience Lab >> Columbia University >> mrv2...@columbia.edu >> >> -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2...@columbia.edu
_______________________________________________ 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.
