Ok that worked. I sent the data for a subject with the skull stripping issue that is common in most of our dataset.
Thanks, Michelle On Fri, Dec 1, 2017 at 4:56 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > try cd'ing to incoming not outgoing (the names are from our perspective I > think :) > > > On Fri, 1 Dec 2017, Michelle VanTieghem wrote: > > >> 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/compli >> anceline . 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 >> >> -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2...@columbia.edu
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