[Freesurfer] using ADNI preprocessed files in FS

Hi,

Sorry for the very basic question but I have not been able to find the answer in the archives, nor anywhere else.

I want to use ADNI data in FS

ADNI data is available in either original DICOM or has been preprocessed in the following manner:

Phillips Systems:

unpreprocessed DICOM N3 corrected

GE and Siemens systems with transmit-receive head RF coils:

unpreprocessed DICOM gradwarped gradwarp plus N3

GE and Siemens systems with receive-only head RF coils:

unpreprocessed DICOM gradwarped gradwarp plus B1 plus N3

I reality there are quite a few more options available. Question is which one to use best for FS (plan is to rerun in a newer FS version)

I suppose that using the files that are gradwarped and B-1 corrected is sensible for using in FS. However the "best" files after quality control have been N3 corrected which makes it a lot easier for me to extract these files from the database (I need a few hundred, meaning I have many thousands of files to extract from).

Would running recon all, but omitting the N3 step be correct ?

Thanks a lot,

JM

Joost Riphagen, MD Phd candidate Maastricht University.