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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 | #First step: measure motion in each run separately, perform the registration, save motion parameters | ||
# 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 \ | ||
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Motion Correction | Motion Correction | ||
for more info, see | for more info, see [[Beauchamp:MotionCorrection|Motion and Distortion Correction]] | ||
Alternative 1: Perform registration to mean image | Alternative 1: Perform registration to mean image | ||
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end | end | ||
Alternative 2:For even greater precision, we Allineate to the hi-resolution anatomical image. | 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 {$ec}EPImean+orig -EPI -cost mi | 3dAllineate -base {$ec}anatSScrop+orig -1Dmatrix_save {$ec}EPI_to_T1.aff12.1D -input {$ec}EPImean+orig -EPI -cost mi | ||
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3dvolreg -prefix NULL -1Dmatrix_save {$ec}r{$r}EPI_to_EPI.aff12.1D -base {$ec}EPImean+orig -input {$ec}r{$r}+orig -cubic | 3dvolreg -prefix NULL -1Dmatrix_save {$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{$r}EPI_to_EPI_to_T1.aff12.1D | cat_matvec {$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{$r}+orig | 3dAllineate -master {$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 | end | ||
