Hi,
This approach is perfectly fine.
All the best,
Mark
On 19 Sep 2012, at 19:00, Chris Keown <[log in to unmask]> wrote:
> My solution to my problem is below. I align my EPI slice to the skull-stripped anatomical. Then I apply this transform to my EPI using a 3mm resampled version of my anatomical as my reference image instead of the original 1mm version. Please let me know if there's anything theoretically wrong with this approach. The results seem to look okay in terms of visual inspection.
> Thanks!
>
> 3dresample -dxyz 3 3 3 -insert ${subj}_anat_brain.nii.gz -prefix ${subj}_anat_brain_resamp.nii.gz
> flirt -ref ${subj}_anat_brain -in coreg_func_slice -out coreg_func_slice_post -omat coregistration_e2a.mat -cost corratio -dof 6 -interp trilinear
> flirt -in ${subj}_resting_moco_ss_b6_LP -ref ${subj}_anat_brain_resamp -out ${subj}_resting_moco_ss_b6_LP_e2a -init coregistration_e2a.mat -applyxfm
>
|