AFNI Tutorial: to3d

In the beginning, a young man is placed upon the scanning table as if in sacrifice. He is afraid; there are loud noises; he performs endless repetitions of a task incomprehensible. He thinks only of the coercively high amount of money he is promised in exchange for an hour of meaningless existence.

The scanner sits in silent judgment and marks off the time. The sap of life rushes to the brain, the gradients flip with terrible precision, and all is seen and all is recorded.

Such is the prologue for data collection. Sent straight into the logs of the server: Every slice, every volume, every run. All this should be marked well, as these native elements shall evolve into something far greater.

You will require three ingredients for converting raw scanner data into a basic AFNI dataset. First, the number of slices: Each volume comprises several slices, each of which measures a separate plane. Second, the number of volumes: Each run of data comprises several volumes, each of which measures a separate timepoint. Third, the repetition time: Each volume is acquired after a certain amount of time has elapsed.

Once you have assembled your materials, use to3d to convert the raw data into a BRIK/HEAD dataset. A sample command:

to3d -prefix r01 -time:zt 50 206 3000 alt+z *000006_*.dcm

This command means: "AFNI, I implore you: Label my output dataset r01; there are 50 slices per volume, 206 volumes per run, and each volume is acquired every 3000 milliseconds; slices are acquired interleaved in the z-direction; and harvest all volumes which contain the pattern 000006_ and end in dcm. Alert me when the evolution is complete."

More details and an interactive example can be found in the following video.