must know usernames and password for all machines that you wish
to transfer files between. You may
need to know IP addresses. Sorry, but for security reasons,
none of that information can be included on this page. File transfer
routines all rely on some knowledge about unix.
visit the "Tranfer Protocols"
page to see examples of telnet, ftp, ssh and scp commands you might
may also wish to visit the Unix Intro
page, of particular interest are the sections on the files
(listing them, using wildcards); the path
(which explains how to move from one directory to another), and
on "copying, moving and removing
files and directories".
from the console to mrisun
Transfers from UMC machines to Campus machines
the Console to Mrisun (Sitting at the Console)
fMRI studies will generate multiple Pfiles, and a couple of structural
NOTE: structural scans (everything but the spiral P files) are automatically
extracted to: /export/home1/sdc_image_pool2/mr_scan
BUT the data is ONLY there until the next exam is collected.
You can also extract the files yourself by going to: /usr/g/bin/res.
Type extract & follow the directions. Files will be sent to /usr/g/insite/tmp.
Click on the toolbox icon (hammer/screwdriver etc.) in the gray control
Service Desktop Manager pops up,
C Shell (lower left), to bring up a shell terminal.
A c-shell terminal will appear. The mouse cursor needs to be inside
the C Shell terminal to be able to type in it. You will need to
transfer anatomical & P files to MRISUN. In the c-shell terminal,
you will need to cd to the appropriate directory
files, are in /export/home1/sdc_image_pool2/mr_scan
(The alias imgdir should get you to the anatomical directory (at
least on MR1)
Functional Pfiles are in /usr/g/mrraw
then ftp to mrisun from that directory.
(Each lab will have their own login account. Contact Ted Trouard
if you need to get an account.)
mrisun, all data should be dumped into an appropriate directory
on /data4 for the user cnl (data2 for some other people).
By convention, each project directory is named for the person running
/data4/cnl/"PI last name"
data should be transferred to the appropriate directory under /data4/cnl.
Again, each person who runs a project should have a directory called
their last name.
may wish to set very liberal permissions for your directories and
files so that they will be easy to access from tommy (where there
is no user "cnl")
do so use the following command:
a directory for your exam, within the appropriate PI directory
to that directory:
(binary mode should be the default)
that the file sizes for both Pfiles AND structural images are correct.
>ls -l | more
-l will give you a long listing of each file in the directory, including
file size. By piping the output of ls -l through more (| more)
you prevent the files from scrolling off the screen. Press the space
bar to go on to the next screen.
Check Pfiles & .MR files: Exist? Does the size match the console
If all of the files are there, and are the same size as they are
on the console, then you can exit from mrisun (type exit) and then
remove the files from the MRI console.
the Console to Mrisun (Sitting at mrisun)
can use ftp to get your files from the console while you are sitting
at mrisun. Simply telnet the relevant console machine:
to the directories where your files are stored and use mget to get
files from Mrisun (UMC) to your Machine
is accessible from any machine that has been given permission to
log on to it. Each principal investigator should check with Ted
Trouard to acquire permission, a username and password. You will
also need mrisun's ip address (same as it was when mrisun was a
sun machine). You can add mrisun's ip address to the host
table on your machine or simply use the ip address instead of the
name. Mrisun is a linux machine that supports telnet/ftp protocols
and ssh/scp protocols.
You can telnet or ftp
from buddy, holly or merlin but CANNOT telnet or ftp TO buddy, holly
or merlin. See information on Clients
and Servers to understand why. You should use ssh
and scp to transfer data
to these machines.
data from mrisun once you have backed it up. (i.e. have tranferred
and confirmed two copies of it somewhere).
the scan sheet to see where it is kept)
to see that the files you expect are in the directory and that they
are the correct sizes (or, at least, not 0 size):
make sure that you have an appropriate directory on the machine
you want to transfer the data TO, and that you know the path to
you are ready to scp to
buddy (or any other machine with an ssh server running). If you
don't have ssh and scp on your machine, then you can use ftp.
Remember, you cannot ftp to buddy, holly or merlin.