File Transfer at UMC

You 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.

Please visit the "Tranfer Protocols" page to see examples of telnet, ftp, ssh and scp commands you might need.

You 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".


Tranfers from the console to mrisun
Transfers from UMC machines to Campus machines


From the Console to Mrisun (Sitting at the Console)

Most fMRI studies will generate multiple Pfiles, and a couple of structural series.
IMPORTANT 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 panel:

The Service Desktop Manager pops up,

Press 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

Anatomical 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

and then ftp to mrisun from that directory.


>ftp mrisun

login (Each lab will have their own login account. Contact Ted Trouard if you need to get an account.)

On 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 the project.

>cd /data4/cnl/"PI last name"

All 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.

You 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")

To do so use the following command:

>site umask 000

Make a directory for your exam, within the appropriate PI directory
>mkdir E12345

cd to that directory:
>cd E12345

>mput P12345
(binary mode should be the default)


>mput E1234*

Check that the file sizes for both Pfiles AND structural images are correct.
>ls -l | more
ls -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 files?
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.

From the Console to Mrisun (Sitting at mrisun)

You can use ftp to get your files from the console while you are sitting at mrisun. Simply telnet the relevant console machine:

>telnet MR1

>telnet MR2

>telnet MR3

Go to the directories where your files are stored and use mget to get them.

Transfer files from Mrisun (UMC) to your Machine

Mrisun 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.

NOTE: 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.

Remove data from mrisun once you have backed it up. (i.e. have tranferred and confirmed two copies of it somewhere).

>telnet mrisun

>ssh mrisun

> cd /data/joe

>cd e#####

(check the scan sheet to see where it is kept)

Check to see that the files you expect are in the directory and that they are the correct sizes (or, at least, not 0 size):

>ls -l

Also 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 that directory.

Now 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.