fMRI data acquisition and storage

Data from the 1.5T Siemens MRI at the Royal University Hospital (RUH) will make it into your hands for analysis in 5 steps:
  1. A volunteer (subject) will lie in the MRI and perform their assigned tasks while the MRI collects image data.(Click here for detailed procedures for operating the RUH MRI to acquire fMRI data.)
  2. The data will be automatically transfered, via DICOM protocol, to the research DICOM linux server named akasha located in the fMRI equipment room at RUH. DICOM is an industry standard for medical images meant to allow the easy transfer of medical images between computers. (Click here for detailed procedures for transfering and converting DICOM images to akasha.)
  3. Using some locally developed software, the DICOM format images will be converted into spr/sdt (stimulate) and HEAD/BRIK (AFNI) formats and stored in the directory:
    /home/fMRI/subject
    where "subject" is the subject number. If you login to akasha as user fMRI you will only see the numbered directories. After the stimulate/AFNI format data is created, the DICOM format data will be tarred and compressed.
  4. The stimulate/AFNI format data will next be copied from akasha to an appropriate analysis computer - currently our analysis computers are thalassa and wilder. Once the stimulate/AFNI format raw data are on the analysis computers, the data will eventually be deleted from akasha's disks. Jennifer will make a backup copy, on CD-ROM or DVD, of the stimulate/AFNI format data. (Click here for detailed instructions on burning the data to cd yourself.) The data will be copied into the fMRI account into the directory:
    researcher/project/subject (see the discussion on File Naming Conventions below for the conventions on directory naming)
  5. You may now analyze your data. Please keep all data under the relevant project directory. This will make it easy to archive the data when you are through.
Note for BioE 898.3 students: The dataset for your project will be stored on a Sun computer named triceratops. You will have to telnet or rlogin to triceratops using procedures that will be given in class. After you login, the data will be in a directory called "project898".

File Naming Conventions

In terms of fMRI data storage, a "subject" is one imaging session with one volunteer. So if you scanned subject number 2403 on November 23, 2148, the data for that particular volunteer would be in:

/home/fMRI/researcher/project/2403

on your analysis linux workstation.

Many investigators will have multiple projects going at the same time. For example, investigator borowsky may have one study on listening and another study on talking. In that case, the project directories would be:

/home/fMRI/borowsky/listening
/home/fMRI/borowsky/talking

If subject 2501 was part of the listening project then the stimulate/AFNI format raw data woiuld be in /fMRI/home/borowsky/listening/2501. And so on. You will end up with a number of subject number directories stored under each project.

More abstractly, the following convention for directory naming for setting up your fMRI data for analysis is suggested:

/home/fMRI/investigator/project/subject

where "investigator" is name of the researcher, "project" is the name of the project and "subject" is the number of the subject. Note that the data in subject directories will be named by task. A task represents an individual imaging "run" of continuous imaging. So the HEAD and BRIK AFNI files for a "run" will be stored abstractly as:

/home/fMRI/investigator/project/subject/task.HEAD
/home/fMRI/investigator/project/subject/task.BRIK

Note that in the AFNI documentation our term "subject" is referred to as a "session". Further suggestions for subsequent directory oragnization are made in the Step-by-step pages.

Frequently, it will happen that one subject will have participated in more than one project will they were in the MRI. In that case, Jennifer will copy the raw data to each of the relevant project directories and then you should manually delete irrelevant data from the subject directories. For example, if subject 2501 did task Rhyme for the listening project and task Guess for the talking project then a copy of /home/fMRI/2501 on akasha will go to to both /home/fMRI/borowsky/listening/2501 and /home/fMRI/borowsky/talking/2501 on the analysis computers. You should then go into /home/fMRI/borowsky/listening/2501 and delete Guess.* and go into /home/fMRI/borowsky/talking/2501 and delete Rhyme.*. This will help to conserve disk space.

Note on data acquired on the old MRI sparc hardware prior to February 2002.

The old Sun workstation formerly known as akasha has been renamed triceratops and an Intel based linux machine has taken over the name of akasha. The switch was necessary because the CPU change in the MRI (from the February 2002 upgrade) makes the data from the MRI incompatable with the Sun sparc data format (a "big endian"/"little endian" hassle). You may continue to analyze your old data on triceratops. The old data on triceratops are available through the user account "fMRI" and, as need arises, will be stored in the old directory organization of /home/fMRI/investigator/date/project/subject where "date" reflects the date of the data acquisition. All of the old data are archived to CD-ROM and can be reloaded onto triceratops or onto a linux machine of your choice - please contact Jennifer Hadley if you need data reloaded.
Back to U of S fMRI web page.