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Beauchamp:Retinotopy: Difference between revisions
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Here are some processing steps to analyse this 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 \ | 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 | ||
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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 | |||
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 | ||
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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 | |||
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 | |||
3dDFT -prefix {$ec}r{$r}vrdtblFFT -detrend junkr{$r}+orig | 3dDFT -prefix {$ec}r{$r}vrdtblFFT -detrend junkr{$r}+orig | ||
end | end | ||
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end | end | ||
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 | |||
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 | |||
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 | |||
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 | |||
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 | |||
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 \ | ||
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-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 | |||
3dbucket -prefix {$ec}Ret -fbuc {$ec}rallvrdtblFFTMAGSTAT+orig junkeccavg+orig junkpolavg+orig \ | 3dbucket -prefix {$ec}Ret -fbuc {$ec}rallvrdtblFFTMAGSTAT+orig junkeccavg+orig junkpolavg+orig \ | ||
{$ec}r{$r}vrdtblFFTf5+orig.HEAD {$ec}r?vrdtblFFTf5flip+orig.HEAD | {$ec}r{$r}vrdtblFFTf5+orig.HEAD {$ec}r?vrdtblFFTf5flip+orig.HEAD | ||
