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Beauchamp:Retinotopy: Difference between revisions
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(New page: {{Beauchamp Navigation Bar}} <br> ==Phase-Mapped Retinotopy== Visual areas are retinotopic. An efficient way to map visual areas is to present stimuli that traverse the visual field. Her...) |
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# create average EPI image to register to | # 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 \ | 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 {$ec}r8+orig.HEAD | {$ec}r6+orig.HEAD {$ec}r7+orig.HEAD {$ec}r8+orig.HEAD | ||
3dTstat -mean -prefix {$ec}EPImean {$ec}rall+orig.HEAD | 3dTstat -mean -prefix {$ec}EPImean {$ec}rall+orig.HEAD | ||
# perform registration | # perform registration | ||
foreach r (1 2 3 4 5 6 7 8) | 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{$r}vr.1D -cubic | 3dvolreg -prefix {$ec}r{$r}vr -base {$ec}EPImean+orig -input {$ec}r{$r}+orig -1Dfile {$ec}r{$r}vr.1D -cubic | ||
end | end | ||
# remove quadratic trend from each run separately | # remove quadratic trend from each run separately | ||
foreach r (1 2 3 4 5 6 7 8) | foreach r (1 2 3 4 5 6 7 8) | ||
3dDetrend -prefix {$ec}r{$r}vrdt -polort 2 {$ec}r{$r}vr+orig | 3dDetrend -prefix {$ec}r{$r}vrdt -polort 2 {$ec}r{$r}vr+orig | ||
end | end | ||
# blur slightly | # blur slightly | ||
foreach r (1 2 3 4 5 6 7 8) | 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 | 3dmerge -doall -1blur_rms 3 -prefix {$ec}r{$r}vrdtbl {$ec}r{$r}vrdt+orig | ||
end | end | ||
rm junk* | rm junk* | ||
foreach r (1 2 3 4 5 6 7 8) | foreach r (1 2 3 4 5 6 7 8) | ||
# Convert to float as required by DFT | # Convert to float as required by DFT | ||
3dcalc -prefix junkr{$r} -datum float -a {$ec}r{$r}vrdtbl+orig -expr "a" | 3dcalc -prefix junkr{$r} -datum float -a {$ec}r{$r}vrdtbl+orig -expr "a" | ||
# perform FFT on each run separately | # perform FFT on each run separately | ||
3dDFT -prefix {$ec}r{$r}vrdtblFFT -detrend junkr{$r}+orig | 3dDFT -prefix {$ec}r{$r}vrdtblFFT -detrend junkr{$r}+orig | ||
end | end | ||
foreach r (1 2 3 4 5 6 7 8) | foreach r (1 2 3 4 5 6 7 8) | ||
# Retinotopic stimulus has periodicity at frequency 5, calculate phase at only that frequency | # 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" | 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 | 3drefit -sublabel 0 FFTr{$r}f5 -subrepkey 0 FFTr{$r}f5 {$ec}r{$r}vrdtblFFTf5+orig | ||
# Calculate magnitude squared at all frequencies | # 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" | 3dcalc -datum short -prefix {$ec}r{$r}vrdtblFFTMAG -cx2r ABS -a {$ec}r{$r}vrdtblFFT+orig -expr "a*a" | ||
end | end | ||
# Average magnitude squared across runs | # Average magnitude squared across runs | ||
3dMean -prefix {$ec}rallvrdtblFFTMAG {$ec}r?vrdtblFFTMAG+orig.HEAD | 3dMean -prefix {$ec}rallvrdtblFFTMAG {$ec}r?vrdtblFFTMAG+orig.HEAD | ||
# Calculate Fratio between frequency of interest and neighboring frequencies | # Calculate Fratio between frequency of interest and neighboring frequencies | ||
rm junk* | rm junk* | ||
3dcalc -prefix junkMAGSTAT -a3 {$ec}rallvrdtblFFTMAG+orig -b4 {$ec}rallvrdtblFFTMAG+orig -c5 {$ec}rallvrdtblFFTMAG+orig \ | 3dcalc -prefix junkMAGSTAT -a3 {$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 )" | -d6 {$ec}rallvrdtblFFTMAG+orig -e7 {$ec}rallvrdtblFFTMAG+orig -expr "c^2 / ( (a^2 + b^2 + d^2 + e^2)/4 )" | ||
# Convert to fbuc | # Convert to fbuc | ||
3dbucket -prefix {$ec}rallvrdtblFFTMAGSTAT -fbuc junkMAGSTAT+orig | 3dbucket -prefix {$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 | # 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 {$ec}rallvrdtblFFTMAGSTAT+orig | 3drefit -sublabel 0 Significance -substatpar 0 fift 16 64 -subrepkey 0 Significance {$ec}rallvrdtblFFTMAGSTAT+orig | ||
# Calculate appropriate phases | # Calculate appropriate phases | ||
# flip CW and CON runs | # flip CW and CON runs | ||
foreach r (3 4 7 8) | foreach r (3 4 7 8) | ||
3dcalc -datum short -prefix {$ec}r{$r}vrdtblFFTf5flip -a {$ec}r{$r}vrdtblFFTf5+orig -expr "-a" | 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 | 3drefit -sublabel 0 FFTr{$r}f5flip -subrepkey 0 FFTr{$r}f5flip {$ec}r{$r}vrdtblFFTf5flip+orig | ||
end | end | ||
# Average together | # Average together | ||
rm junk* | rm junk* | ||
3dcalc -prefix junkeccavg -datum short -a {$ec}r2vrdtblFFTf5+orig -b {$ec}r4vrdtblFFTf5flip+orig \ | 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)" | -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 \ | 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)" | -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 | # 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 {$ec}r?vrdtblFFTf5flip+orig.HEAD | 3dbucket -prefix {$ec}Ret -fbuc {$ec}rallvrdtblFFTMAGSTAT+orig junkeccavg+orig junkpolavg+orig {$ec}r{$r}vrdtblFFTf5+orig.HEAD {$ec}r?vrdtblFFTf5flip+orig.HEAD | ||
