Hello FSL Experts,
I am trying to run a PPI analysis and to do so, I need to transform an 8mm radius spherical ROI mask to each subject's native space. I have tried multiple times using FLIRT to do so with the following command:
flirt -in roimask.nii.gz -ref subjects_filtered_func_data.nii.gz -out transformedroimask.nii.gz -omat matrix -dof 6
Every time the output mask is in the completely wrong space (e.g., in the left basal ganglia when the original mask is in the right prefrontal cortex). Is there anything I can do to get the ROI mask in the right place? I tried using different DOF but that made things worse. I do not want to make a mask, manually, for each individual subject, which is the alternative to doing this. I am grateful for any advice you can offer.
Best,
Dave
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