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Hi Freesurfer community,

I am currently running Freesurfer 6.0 and have run a number of 3T MPRAGEs through recon-all. I have also run these with the -mprage and -3T flags to compare outputs.

I have therefore ended up with four runs of the same test patients:

1) Without flags

2) With the -3T flag only

3) With the -mprage flag only

4) With both the -3T and -mprage flag (in terms of order of operations I had the mprage flag then the 3T flag)

However, when checking the outputted volume and CT measurements the values for the run 2 (just 3T flag) and the run 4 (with both flags) produce identical measurements. Does this mean that the mprage flag does not operate in the presence of the 3T flag? It was my assumption that the two flags call very different changes to the recon-all pipeline (-3T affects Taliarch atlas used and the nuintensity correction whilst -mprage affects mri_segment and mri_normalize parametres).

In this case is there still any benefit in running both of the flags or is the 3T flag making the mprage flag redundant?

Best wishes Dan

Daniel King

PhD Candidate in Neurosciences, School of Life and Health Sciences & Aston Brain Centre (SW505), Aston University, Aston Triangle, B4 7ET West Midlands, UK

Email: kingdj@aston.ac.ukmailto:kingdj@aston.ac.uk Twitter: @danieljking8