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 are three snapshots of an eccentricity mapping stimulus:

Over the course of a 5-minute scan series, the ring expands from central to peripheral five times.

Here are three snapshots of a polar angle mapping stimulus:

Over the course of a 5-minute scan series, the wedge rotates around the fixation point five times.

Processing Phase-Mapped Retinotopy Data in AFNI

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

First step: measure motion in each run separately, perform the registration, save motion parameters 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

Motion Correction

for more info, see Motion and Distortion Correction

Alternative 1: Perform registration to mean image

 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

Alternative 2: For even greater precision, we Allineate to the hi-resolution anatomical image.

 3dAllineate -base {$ec}anatSScrop+orig -1Dmatrix_save {$ec}EPI_to_T1.aff12.1D -input  {$ec}EPImean+orig -EPI -cost mi

 foreach r (1 2 3 4 5 6 7 8)
 3dvolreg -prefix NULL -1Dmatrix_save {$ec}r{$r}EPI_to_EPI.aff12.1D -base {$ec}EPImean+orig  -input {$ec}r{$r}+orig  -cubic
 cat_matvec {$ec}EPI_to_T1.aff12.1D  {$ec}r{$r}EPI_to_EPI.aff12.1D >  {$ec}r{$r}EPI_to_EPI_to_T1.aff12.1D
 3dAllineate -master {$ec}anatSScrop+orig -mast_dxyz 2.0 -1Dmatrix_apply {$ec}r{$r}EPI_to_EPI_to_T1.aff12.1D \
 -input  {$ec}r{$r}+orig -final quintic -prefix {$ec}r{$r}vr+orig 
 end

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

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

Average magnitude squared across runs

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

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 )"

Convert to fbuc

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

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

Calculate appropriate phases 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

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)"

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

Here are flat maps showing the thresholded eccentricity and polar angle maps produced by this analysis: