Dear All,

 

Excuse the basic nature of these quetions. I coregistered 2 analyze volumes in SPM (pre and post resection MR scans for same patient) with cost function masking. I imported the preresection scan in Freesurfer, and processed it with recon -all.

1) What transform matrices should I multiply the postresection scan to get it in the FS space in alignment with the processed preresection MR, and where do I find them?

2) Once in FS, how do I crop/mask the posteresection volume using saggittal, coronal or axial planes of my choosing? (I am interested in generating a small cube containing the posteresection volume, then extracting the postresection volume itself by intensity threshold (CSF vs surronding cavity wall brain) and masking with preresection MR pial surface laterally).

 

Please advise,

 

Octavian.