In order to get your data into SPM2 you will need to reconstruct your data, from it's original P-File format, convert it to AFNI format, slice-time correct your data in AFNI (optional), and convert it to ANALYZE FORMAT.

Note: These commands must be run on via command line interaction with the MOSICS cluster (i.e. Datil, Jalapeno, or Cayenne).

For a more in-depth description of the steps involved with reconstruction, conversion to AFNI, and slice-time correction, please visit Tom Johnstone's AFNI webpage.

Reconstruct your Data

• Run 'sip filename.SIF'
  If you have not done this before it is best you visit Tom Johnstone's AFNI webpage.
• After it begins to spit out data you want to kill it (Ctrl+C).
• You now want to go into your .SIF file and edit the scaling factor to be the square-root of hte maximum value it outputted.
• Run 'sip filename.SIF' (let it run this time)
• This will create a folder containing a .sdt file for each run.

Convert to AFNI format

• Run Tom Johnstone's 'afnigui'
• Use the 'convert to AFNI format (to3d)' function (selected form the menubar)
• Select the working directory that contains your .sdt file
• Select the .sdt file you would like to construct
• Select a prefix you would like to apply to your AFNI file
• Click the load header information automatically
• Select the number of scans you would like to discard
• Make sure that 'epan' is slelected.
• Click 'View Command'
• Click 'Append to Batch Script'
• When you have followed these steps for each AFNI file you require Select the 'batch script' function and click 'execute batch script'.

Slice-Time Correction (optional)

• Run Tom Johnstone's 'afnigui'
• Use the 'slice timing correction' function (selected form the menubar)
• Select the working directory that contains your AFNI file
• Choose the AFNI file you would like to Slice-Time Correct
• Select a prefix you would like to apply to your slice-time corrected AFNI file
• Click 'View Command'
• Click 'Append to Batch Script'
• When you have followed these steps for each AFNI file you require Select the 'batch script' function (from the menubar) and click 'execute batch script'.

Convert to (SPM2 compatible) ANALYZE format.

• Convert the desired images to axial slices via:
  3daxialize -prefix YOUR_PREFIX -orient LPI PATH_TO_ORIGINAL_FILE
• Convert the desired images to ANALYZE format via:
  3dAFNItoANALYZE ANALYZE_PREFIX AFNI_FILE
  Note: Unlike AFNI, ANALYZE format represents each time point with a seperate file; such that this command will generate a seperate file for each scan in your time-series.