Setting up the Files

1. Setting up the directory

• Make a directory for your subject, and put the following subdirectories in it
air
segment
loadret
raw

2. Structural data

• Copy all structural data to the segment subdirectory
 

3. AIRing functional data

• You need to be aware of byte swapping. If your scanner and UNIX processing machine both byte-swap the same, then you should never need to byteswap. Otherwise, you might! For the example data, you do need to swap in these steps below.
  
• Copy all functional data to the raw subdirectory.
• Epi2analyze the gre structural volume acquired immediately after the FSE structural scan (#4 in the scanning webpage). This will be the volume that you align to.
epi2analyze HC-Subj+8+2+1_001.img SubjFirstVolume 3 -x 128 56 -s
(Note, the "-s" option is for byte swapping, which will need to be done on the example data if you have a DEC, but not so if you have a SUN/SGI. For your data, it will depend on if the scanner UNIX is compatible with your computer UNIX)
• In the air directory, make a subdirectory for each run:
air/run1
air/run2
etc.
• For each run, enter the air/run directory, and run the air command, aligning to the volume you just epi2analyzed. Be sure to check if you need to byte swap or not (the first y/n option is for byte swapping, again y for DEC, n for SGI/SUN with my sample data).
cd air/run1
AIR ../../raw/HC-Subj+2097+8+2+1_001 run1 116 3 160 y 128 1 y 0 0 ../../raw/SubjVolume001 &

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