161
edits
Beauchamp:Retinotopy: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
→Processing Phase-Mapped Retinotopy Data in AFNI
| Line 65: | Line 65: | ||
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 | Give it correct stats--numerator degrees of freedom is 2*number of runs, denominator degrees of freedom is 8*number of runs: | ||
3drefit -sublabel 0 Significance -substatpar 0 fift 16 64 -subrepkey 0 Significance {$ec}rallvrdtblFFTMAGSTAT+orig | 3drefit -sublabel 0 Significance -substatpar 0 fift 16 64 -subrepkey 0 Significance | ||
Calculate appropriate phases | {$ec}rallvrdtblFFTMAGSTAT+orig | ||
Calculate appropriate phases by first flipping clockwise (CW) and contracting (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" | |||
3drefit -sublabel 0 FFTr{$r}f5flip -subrepkey 0 FFTr{$r}f5flip {$ec}r{$r}vrdtblFFTf5flip+orig | |||
end | |||
Average together | Average together the flipping CW and CON runs with the counterclockwise (CCW) and expanding (EXP) runs respectively: | ||
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 \ | ||
| Line 79: | Line 79: | ||
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 | 3dbucket -prefix {$ec}Ret -fbuc {$ec}rallvrdtblFFTMAGSTAT+orig junkeccavg+orig junkpolavg+orig | ||
{$ec}r?vrdtblFFTf5+orig.HEAD {$ec}r?vrdtblFFTf5flip+orig.HEAD | {$ec}r?vrdtblFFTf5+orig.HEAD {$ec}r?vrdtblFFTf5flip+orig.HEAD | ||
