Hi FSusers,

I am engaging to map automatic segmentation image (eg. aparc.a2009s+aseg.mgz) to raw functional space. According to the instructions from the FreeSurfer website, I found that there were two ways below to do it. However, the results from both methods are different and attached. Let me say BNC006 is a subject under $SUBJECTS_DIR (here /drive3/TEST). The functional data has been processed using FSL and found in bold.feat directory.

*# one way* (red images in the attached picture) $ bbregister --mov example_func.nii.gz --bold --s BNC006 --init-fsl --reg register.dat $ mri_label2vol --seg BNC006/mri/aparc.a2009s+aseg.mgz --temp example_func.nii.gz --reg register.dat --fillthresh 0.5 --o BNC006 .aseg-in-fun.nii.gz

*# anther way* (blue images in the attached picture) $ reg-feat2anat --feat /drive3/TEST/BOLD/bold.feat --subject BNC006 $ aseg2feat --feat /drive3/TEST/BOLD/bold.feat --aseg aparc.a2009s+aseg cd /drive3/TEST/BOLD/bold.feat/reg/freesurfer

*BNC006 .aseg-in-fun.nii.gz* and *aparc.a2009s+aseg.nii.gz* are outputs from the first and second one, respectively. Does anyone give me some suggestion about which method is suitable to my situation.

Best, Liang