• To start a new MRI session with the 3T Siemens, choose 'Register' from the 'Patient' menu. You will be asked to input information such as weight, date of birth, and patient ID.
1. Patient ID: You can use a few words or numbers to identify the study. The last word of the Patient ID is your lab name. For example, if you are a member of the group 'jodlab' then you could use a name like 'exp22 subj13 jodlab'. The name of your lab should be separated from the other parts of the ID with a period, space or comma.
2. You may want to de-identify your DICOM data. If so, do not enter the participants name as the patient name (enter your identification code number). If you want full HIPAA deidentification compliance you should also only specify the birthdate to the nearest year (e.g. if the person was born on March 3, 1977, then make the date of birth January 1, 1977.
3. You may want to place a fiducial marker on the participant so you do not confuse the left-right side. I use vitamin-E capsules (stored by the sink in the research room). These appear on the anatomical scan but not on the fMRI scans (if you want a fiducial to appear on fMRI you will need CuSO4 markers, however as long as you have a marked anatomical you can infer the left-right of a fMRI scan).

1. On the scanner, choose 'Browser' from the 'Patient' list. Select the patient you want and choose the different scans you wish to store by clicking on the scan with the CTRL key depressed. 
2. Note: we suggest transferring data from one person at a time - that way they will be stored separately on the server.
3. Once you have selected the files you want to move, select 'Transfer to...' from the 'Transfer' menu and select USC.

C. Getting data from the server

1. Use an SSH client to securely get your data. An example is winSCP (Windows), kbear (Linux)  or OpenSSH (this is installed on all modern Macs)
2. To set up a connection with winSCP if your labname is jodlab and your password was qwerty@321:
1. Start winSCP, press 'New', hostname (enter the server IP address, i.e. 172.17.*.*), port 22, username jodlab, password qwert@321, and then press Save
2. Now when you relaunch winSCP you can simply click on the server's name to connect.
3. If you entered your lab name when you collected the data (see A.1 above), your data will be in your home folder (e.g. if you ran the study at 1:32pm on January 9, 2006, and you are part of the jodlab, your data will be saved as '\home\jodlab\20060109_133248.tgz'). You can copy the file to your computer (drag and drop with winSCP). 
4. If you did not enter the lab name when you collected the data (see A.1 above), then your data will be in the \home\guest\ folder, e.g. '\home\guest\20060109_133248.tgz'. Please do not leave data in the guest folder more than a month. If the guest folder becomes too cluttered, we will remove files.

D. Converting your DICOM images to Analyze/NIfTI

E. Technical notes

Data is stored on a 1.6 terabyte RAID 5 disk array. The redundant storage should protect against any data loss. DICOM transfers use the free DCMTK storescp program. The program automatically alerts my data compression and archiving software after each session is transferred: storescp -v -ss p -xcs "dicompress #p" -tos 4 -aet USC 104 All the images from a participant are saved to a single compressed archive using Chris Rorden's DICOMpress software. This software also sorts the archives into each user's personal folder. File names are based on the study date and time listed in DICOM tags 0008:0020 and 0008:0030.