Hi,

I am trying to process 7T MPRAGE data (not MP2RAGE) using recon-all. In previous threads, a few people have suggested using SPM to correct for bias first and then running recon-all. Alternatively I saw a thread which suggests modifying the mri_nu_correct command

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61913.html

Can I edit the recon-all to run this alternative command and simply run recon-all?  The threads are all really old and SPM is now SPM12 which integrates things. Is this modified bias correction inside FS as good as SPM ? I am mainly interested in thalamic segmentation.

Are there others with the same issue?

Thanks

manoj