SPM DATA ANALYSIS
T2 parameters for language 1. RECONSTRUCTION
  26 slices   PSP
  Xres=512   type psp, one level up from /raw directory
  Yres=512   working dir= .
  slice thickness=5mm   # of tasks= # of P files
  FOV=240   name of task(s)=
  recon P files=yes
T2 parameters for motor  
  24 slices   for each task
  Xres=512   # of slices=
  Yres=512   # of skips=0
  slice thickness=3mm   # of acquisitions= # of TR's acquired for the task
  FOV=240   Xres=
  Yres=
MPRAGE parameters   FOV=
  124 slices or locs   slice thickness=
  Xres=256   slice orientation=axial
  Yres=256   slices acquired=I->S
  slice thickness=1.3mm  
  FOV=240   convert T2=yes or no
  convert SPGR=yes or no
EPI or FUNCTIONAL parameters   dir holding P files=raw
  MOTOR  
  24 slices   when psp is done, type movescratch.sh, space, and the number of images you want removed from the beginning of 
  Xres=80   ALL the functional runs (e.g., to remove the first five images (or 10 seconds) of the experiment, type movescratch.sh 5)
  Yres=80    
  slice thickness=3mm
  FOV=240 2. REALIGNMENT
  voxel=3mm   click REALIGN
    # subjects=
  NON-MOTOR   # sessions (runs)=
  26 slices   select images for realignment; cd to /subject/functional/task_name/SPM_material
  Xres=64   
  Yres=64    choose options
  slice thickness=5mm   Coregister and Reslice
  FOV=240   All images and Mean Image
  voxel=3.75mm  
3. SMOOTHING
  click SMOOTH
  smoothing in mm=(twice the size of a single voxel; 6 for motor and 8 for non-motor)
 
  select the "r" images in /subject/functional/task_name/SPM_material you want to smooth
 
4. MODEL DESIGN AND ASSOCIATING DATA WITH MODEL
  click FMRI
  choose Design
  interscan interval=2 (or your TR)
  scans per session=total mumber of TR's, minus five, for 
  each run, separated by a space (e.g., for 3 runs of 197 TR's  each, enter 192 192 192)
 
  specify design in=scans or seconds
  base set at=hrf
  model interactions=no
  # of conditions= # of conditions you are testing or modeling in each run
  name of condition=name of first condition, second condition ...
  vector of onsets=all of the starting points of this condition
  duration=duration of each block of this condition
  parametric modulation=none
  other regressors=0
 
  model design output is SPM.mat; make a copy of this model, giving it a descriptive name, for use with other subjects
  
  ASSOCIATING DATA WITH MODEL
  click FMRI
  choose Data
  then select the SPM.mat file you just created, or a copy of the model from another experiment
  select functional images for each run with an "r" prefix if you're not smoothing, or images with an "sr" prefix if you are smoothing
 
  remove global effects=scale
  high-pass filter=specify  accept what SPM gives you
  correct for serial=none
 
  output is the experiment's design matrix
 
5. ESTIMATE
  click ESTIMATE
  choose the SPM.mat file that is the ouput of Associating Data with Model
 
6. RESULTS
  click RESULTS
  choose the same SPM.mat file
  create a T contrast
  mask with other contrasts=no
  select desired threshold