Beauchamp:Retinotopy

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Phase-Mapped Retinotopy

Visual areas are retinotopic. An efficient way to map visual areas is to present stimuli that traverse the visual field. Here is a sample eccentricity mapping stimulus: File:Beauchamp eccstim.png

Here is a sample polar angle mapping stimulus: File:Beauchamp polstim.png

Processing Phase-Mapped Retinotopy Data in AFNI

Here are some processing steps to analyse this data in AFNI:

1. First step: measure motion in each run separately, perform the registration, save motion parameters
2. create average EPI image to register to

 3dTcat -prefix {$ec}rall {$ec}r1+orig.HEAD {$ec}r2+orig.HEAD {$ec}r3+orig.HEAD {$ec}r4+orig.HEAD {$ec}r5+orig.HEAD \
 {$ec}r6+orig.HEAD {$ec}r7+orig.HEAD {$ec}r8+orig.HEAD
 3dTstat -mean -prefix {$ec}EPImean {$ec}rall+orig.HEAD

1. perform registration

 foreach r (1 2 3 4 5 6 7 8)
  3dvolreg -prefix {$ec}r{$r}vr -base {$ec}EPImean+orig  -input {$ec}r{$r}+orig  -1Dfile {$ec}r{$r}vr.1D -cubic
 end

1. remove quadratic trend from each run separately

 foreach r (1 2 3 4 5 6 7 8)
  3dDetrend -prefix {$ec}r{$r}vrdt -polort 2  {$ec}r{$r}vr+orig
 end

1. blur slightly

 foreach r (1 2 3 4 5 6 7 8)
  3dmerge -doall -1blur_rms 3 -prefix {$ec}r{$r}vrdtbl {$ec}r{$r}vrdt+orig 
 end
 rm junk*
 foreach r (1 2 3 4 5 6 7 8)
 # Convert to float as required by DFT
  3dcalc -prefix junkr{$r} -datum float -a  {$ec}r{$r}vrdtbl+orig -expr "a"
   # perform FFT on each run separately
   3dDFT -prefix {$ec}r{$r}vrdtblFFT -detrend junkr{$r}+orig
 end

 foreach r (1 2 3 4 5 6 7 8)
 # Retinotopic stimulus has periodicity at frequency 5, calculate phase at only that frequency
  3dcalc -datum short -prefix {$ec}r{$r}vrdtblFFTf5 -cx2r PHASE -a {$ec}r{$r}vrdtblFFT+orig'[5]'  -expr "a"
  3drefit -sublabel 0 FFTr{$r}f5 -subrepkey 0 FFTr{$r}f5 {$ec}r{$r}vrdtblFFTf5+orig
 # Calculate magnitude squared at all frequencies
  3dcalc -datum short -prefix {$ec}r{$r}vrdtblFFTMAG -cx2r ABS -a {$ec}r{$r}vrdtblFFT+orig  -expr "a*a"
 end

1. Average magnitude squared across runs

 3dMean -prefix {$ec}rallvrdtblFFTMAG {$ec}r?vrdtblFFTMAG+orig.HEAD

1. Calculate Fratio between frequency of interest and neighboring frequencies

 rm junk*
 3dcalc -prefix junkMAGSTAT -a3 {$ec}rallvrdtblFFTMAG+orig -b4 {$ec}rallvrdtblFFTMAG+orig -c5 {$ec}rallvrdtblFFTMAG+orig \
 -d6 {$ec}rallvrdtblFFTMAG+orig -e7 {$ec}rallvrdtblFFTMAG+orig -expr "c^2 / ( (a^2 + b^2 + d^2 + e^2)/4 )"

1. Convert to fbuc

 3dbucket -prefix {$ec}rallvrdtblFFTMAGSTAT  -fbuc junkMAGSTAT+orig

1. Give it correct stats--numerator degrees of freedom is 2*number of runs, denominator degrees of freedom is 4*number of runs

 3drefit  -sublabel 0 Significance -substatpar 0 fift 16 64 -subrepkey 0 Significance {$ec}rallvrdtblFFTMAGSTAT+orig

1. Calculate appropriate phases
2. flip CW and CON runs

 foreach r (3 4 7 8)
  3dcalc -datum short -prefix {$ec}r{$r}vrdtblFFTf5flip -a {$ec}r{$r}vrdtblFFTf5+orig  -expr "-a"
  3drefit -sublabel 0 FFTr{$r}f5flip -subrepkey 0 FFTr{$r}f5flip {$ec}r{$r}vrdtblFFTf5flip+orig
  end

1. Average together

  rm junk*
  3dcalc -prefix junkeccavg -datum short -a {$ec}r2vrdtblFFTf5+orig -b {$ec}r4vrdtblFFTf5flip+orig \
  -c {$ec}r6vrdtblFFTf5+orig -d {$ec}r8vrdtblFFTf5flip+orig -expr "mean(a,b,c,d)"
  
  3dcalc -prefix junkpolavg -datum short -a {$ec}r1vrdtblFFTf5+orig -b {$ec}r3vrdtblFFTf5flip+orig \
  -c {$ec}r5vrdtblFFTf5+orig -d {$ec}r7vrdtblFFTf5flip+orig -expr "mean(a,b,c,d)"

1. Combine stats, individual runs, and averages in one file for ease of viewing

  3dbucket -prefix {$ec}Ret -fbuc  {$ec}rallvrdtblFFTMAGSTAT+orig junkeccavg+orig junkpolavg+orig \
 {$ec}r{$r}vrdtblFFTf5+orig.HEAD   {$ec}r?vrdtblFFTf5flip+orig.HEAD