Hi, I am just following up on my prior posts regarding skull strip issues and whether using freesurfer 6.0 would improve over freesurfer 5.3 . I sent the data over the ftp and would greatly appreciate it if you could take a look to see if there is a way to improve the skull strip since we have this issue with 100+ scans and my attempts to use gcut, and other skullstrip programs, has not worked.
Thank you, Michelle On Fri, Dec 1, 2017 at 5:08 PM, Michelle VanTieghem < michelle.vantieg...@gmail.com> wrote: > 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/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: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 > -- 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.
