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Beauchamp:Retinotopy: Difference between revisions
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{$ec}r6+orig.HEAD {$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 | ||
# | |||
Motion Correction | |||
for more info, see #[[Beauchamp:MotionCorrection|Motion and Distortion Correction]] | |||
Alternative 1: Perform registration to mean image | |||
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 | ||
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 | # 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) | ||
