Getting data from the MRI scanner to our system

General Information

In order to start analyzing your data, you will have to retrieve it from the 3T Philips scanner, where it was saved during scanning. The radiographers will save these data immediately after scanning is completed on a computer named “hercules”, located at the 3T Scanner centre. You’ll have to connect to this computer and copy the data to our computers. This protocol describes how to do this.

1. Determine the path to the raw data on hercules

1.1. Go to broca or luria (using XWin32)

1.2. Open a console

1.3. Connect to hercules (the computer at the MRI centre which stores the raw fMRI data) by typing:

ssh -l christoff 142.103.107.25 (NOTE: l is small L)

when asked for password, enter the password which you can find in the scanning log book.

1.4. Now you are on hercules. Go into the raw data directory for our lab, by typing:

cd /data/mrcntr/fMRI/Christoff/

to see what research projects exist, type:

ls

at the prompt. You might see something like:

ANAGRAM DEVELOPMENT rtfmri SART

1.5 Find the research project you would like to retrieve data from and go into its folder, by typing, e.g.:

cd DEVELOPMENT

The data from each scanning session are saved by the date of acquisition, plus description of the project. Once you find the folder you are looking for, go into it by typing, e.g.:

cd Oct05_05_anagramcluster_test

1.6 Verify that all the data you will need is in here, by typing ls at the prompt. Once you’ve confirmed this, view the full directory path to where you are on the hercules system, by typing:

pwd

You may see something like:

/data/par_rec/fMRI/Christoff/DEVELOPMENT/Oct05_05_anagramcluster_test

This is the target directory which you would like to copy over to your analysis directory in our lab. Make a note of it, or copy and paste it into a text file on your computer.

2. Copy the raw data from hercules to your analysis directory

2.1 If you are still connected to hercules, disconnect and return to Jekyll by typing:

exit

at the hercules prompt. If you are unsure which computer you are on, type:

hostname

at the prompt to check.

2.2 Go into the analysis directory on Jekyll where you would like to copy the raw data. This would be a directory on /clabdata or /prodata on Jekyll, e.g.:

cd /clabdata

If you don’t yet have your own analysis directory there, create one, .e.g:

mkdir kamyar

If you don’t already have a directory for this particular project, create one. As you start working on several projects, this might be very useful. Type, e.g.:

cd kamyar
mkdir anagrams

and go in it by typing:

cd anagrams

2.3 Copy the raw data from hercules, using the directory path you determined in I. above. Use secure copy ( scp ) to transfer the data, by typing:

scp -r christoff@142.103.107.25:/<the path you determined above>

For the specific example above, what you type at the prompt (after substituting the path) will look like this:

scp -r christoff@142.103.107.25://data/mrcntr/fMRI/Christoff/DEVELOPMENT/Oct05_05_anagramcluster_test .

The syntax of the scp command requires that you first enter the location of the computer and the full path to the directory FROM which you would like to copy. Last you would enter the directory TO which you would like to copy, in your case, the current directory on Jekyll where you are. In linux, the current directory where you are is indicated by . , hense you ended the scp command by typing . at the end.

When asked for password, enter the same password as in 1.3 above.

2.4 Once all the data is transferred, type ‘ls -l’ at the prompt, to double check what has been transferred. You will notice that the entire directory has been copied, so it will be listed as, e.g.:

Oct05_05_anagramcluster_test

go in it by typing:

cd Oct05_05_anagramcluster_test

and you will see your raw data, now copied onto your analysis directory and ready for the next step (Converting raw Philips data to SPM format).