|
|
| Line 33: |
Line 33: |
| Motion Correction | | Motion Correction |
|
| |
|
| 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. 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)
| |
| 3dvolreg -prefix {$ec}r{$r}vr -base {$ec}EPImean+orig -input {$ec}r{$r}+orig -1Dfile {$ec}r{$r}vr.1D -cubic
| |
| end
| |
| | |
| Alternative 2: For even greater precision, we Allineate to the hi-resolution anatomical image.
| |
| 3dAllineate -base {$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 |
