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/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
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contains patient information, please contact the Partners Compliance HelpLine at
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