MOTION CORRECT THE DATA USING MC-SESS You will next motion correct Bert s functional data. Motion correction is optional, however if you do motion correct the data, you will still be able to choose whether to use the raw or motion corrected data later in the analysis stream. Motion correction is recommended since it allows you to determine how much motion there was during the scan.

The mc-sess script uses the AFNI motion correction algorithm to align all the images in a session to the first time image of the first run. This command will motion correct any sessions specified in the sessid and sesspar files of your Study Directory, so in this case, only Bert will be motion corrected.

To motion correct, you would go to your Study Directory and type:

mc-sess -sf sessid -df sesspar

The motion correction takes approximately 30 minutes.

OUTPUT: The mc-sess command creates a new functional volume in each of Bert s functional runs. This new volume will have the same size as the raw volume, but will have stem fmc instead of f . Here is what you should now see if you do an ls for Bert s functional run 007:

xxx[123]  ls 007
f.bhdr         f_014.hdr     fmc_008.bshort
f_000.bshort   f_015.bshort  fmc_008.hdr

TIP: All the options for any FS-FAST command can be displayed by typing the command by itself (e.g. mc-sess ) at the prompt.

The fmc.mcdat text file: A text file called fmc.mcdat will also be showing in each run subdirectory. The motion correction parameters are stored in this file. For example, on the next page we show what the fmc.mcdat file should look like for Bert s run 007.

Here is the beginning of Bert s fmc.mcdat file for bold/007:

0 0.000 -0.000 0.000 -0.000 0.000 -0.000 0 0 0.000 1 0.018 -0.002 0.012 -0.023 0.012 -0.031 9.813 9.792 0.040 ...

Each row of the fmc.mcdat text file corresponds to a different time point. There are ten columns in any fmc.mcdat file-- (1) (2) (3) (4) (5) (6) (7) (8) (9) (10) --corresponding to various parameters: (1) time point number (2) roll rotation (in ) (3) pitch rotation (in ) (4) yaw rotation (in ) (5) between-slice motion or translation (in mm) (6) within slice up-down motion or translation (in mm) (7) within slice left-right motion or translation (in mm) (8) RMS error before correction (9) RMS error after correction (10) total vector motion or translation (in mm)

Those who use this program should cite Cox RW and Jesmanowicz A. Real-time 3D image registration for functional MRI. Magnetic Resonance in Medicine, 42: 1014-1018; 1999. This data file can be plotted using gnuplot or another plotter (e.g. by exporting and plotting in Excel).