1. Create a symbolic link to your mri directory.
Create a link from your home (username) directory to your mri  folder that is located in your unix partition (h#) by typing the following from your home directory:

            

maroon/h#/username>> ln -s /maroon/h#/mri so that the following appears in your home directory when         you type 'ls -l': maroon/h#/username>> mri -> /maroon/h#/mri

You will need to do this only once.

2.  From the scanner, raw data (anatomies and pfiles) should be put by the scanner operator into your mri directory on your maroonpartition so that they appear named by date and session:

/maroon/h#/username/mri/raw/040201a  (in the linked directory) or /maroon/h#/mri/raw/040201a     (in the original directory)

3.  Raw data (anatomies and unreconned Pfiles) should be left  here overnight so that they are backed up by the automated system.  Therefore, should you lose raw data and need to recover it, contact Martin Frost at me@cs.stanford.edu ,who can obtain a copy from the backup.

Copying Pfiles
1.  Mapping your maroon partition.
You will need to make a connection to the data in its directory on maroon from the PC you will useto backup and recon your data.

From Rojo (or an equivalent PC with aCD burner)right click on the computer icon (which may be named 'My Computer'or the actual name of that computer, 'Blue') and left-click on Map Network Click Browse Entire Network. Double click Hummingbird NFS. Then doubleclick maroon.stanford.edu. Highlight your partition ('h3',e.g.) and click OK. Back in themainwindow, click Finish.

You will not need to map the network connection again to a particular machine once you have done it once.

2.  Now copy files (whole session directory, i.e. 040201a) by dragging from maroon to Rojo (or other local machine).

mrInitRet

Run mrInitRet to set up the directory tree and data structures needed for mrLoadRet. This also creates a Readme.txt file.

Alignment

Perform the alignment with mralign .

Copy Readme.txt file to scanner-log database Save a copy of the readme file to: maroon/h1/heeger/public_html/labmanual/scanner-log/ReadmeFiles renamed readme-yyyy-mm-dd-s , where s is the session letter code (e.g. readme-2001-06-13-a)

Transfer display code
Using fetch or ftp, transfer every matlab function included in the display code used to run the stimulus for the scan you are preparing to a directory in your scan directory labelled 'Display Code.'

Burn CD's
 

1.  BlankCD's are located in the tall metal cabinet outside the fishbowl. 2.  Insert blank CD into CD writer drive. 3.  Run Adaptec Easy CD Creator .  When the window opens, click DataCD 4.  Drag files you wish to copy to window on lower left from window on upper left.  Include entire session directory. 5.  Name CD with session name (i.e. 040201a) in boldheaderfieldin lower left window. 6.  Click Create CD icon on menu bar. 7.  Run at 8x rate.  Create only.  Click ok .   If you get a buffer error        message, reduce rate to 4x and try again with a new CD. 8.  Store 1 copy of CD with its readme file in binderin metal cabinet.

Clean Up
1.  Once the coranal has been computed, the tSeries and Pfiles maybe deleted.  Alternatively, Pfiles may be zipped and not deleted.

2.  Data should now be moved from PC to permanent location on maroon.