Hi,
I am following up again -- 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 on Dec 1 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 8, 2017 at 12:31 PM, Michelle VanTieghem < michelle.vantieghem@gmail.com> wrote:
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.vantieghem@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 fischl@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 < fischl@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 attachedscreenshot.
Thanks! M On Fri, Dec 1, 2017 at 4:26 PM, Bruce Fischl <fischl@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 <fischl@nmr.mgh.harvard.edu> wrote: Hi Michelle
probably best to tar and gzip the entiresubject directory and ftp it to us:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers Bruce On Sat, 18 Nov 2017, Michelle VanTieghemwrote:
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 fischl@nmr.mgh.harvard.edu wrote: Hi Michelle
are you doing anything out ofthe 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, MichelleVanTieghem wrote:
Hello, I have posted severaltimes 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 colleaguesuggested this may be due to versions: that 6.0 deals with skull stripping much better than 5.3.
I wanted to ask ifindeed 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 inPsychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
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-- Michelle VanTieghem PhD student in Psychology Developmental AffectiveNeuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu