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Beauchamp:Retinotopy: Difference between revisions
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→Processing Phase-Mapped Retinotopy Data in AFNI
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Before analyzing the retinotopy data, motion correct by aligning all EPIs to the mean EPI and registering that to the high-res anatomy, both in a single step to reduce noise. For more info, see [[Beauchamp:MotionCorrection|Motion and Distortion Correction]] | Before analyzing the retinotopy data, motion correct by aligning all EPIs to the mean EPI and registering that to the high-res anatomy, both in a single step to reduce noise. For more info, see [[Beauchamp:MotionCorrection|Motion and Distortion Correction]] | ||
Remove quadratic trend from each run separately: | Remove the 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 each run 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* | ||
Convert to float as required by DFT, and then perform FFT on each run separately: | |||
foreach r (1 2 3 4 5 6 7 8) | foreach r (1 2 3 4 5 6 7 8) | ||
3dcalc -prefix junkr{$r} -datum float -a {$ec}r{$r}vrdtbl+orig -expr "a" | |||
3dDFT -prefix {$ec}r{$r}vrdtblFFT -detrend junkr{$r}+orig | |||
end | end | ||
