Alex,
The -washu_mprage flag affects mri_normalize and mri_segment. It adjusts the parameters of those binaries to match the assumed intensity profile in mprage scans, eg. to account for darker grey matter. I've updated the help text in recon-all.
Nick
As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...)
Many Thanks!
-Alex Li Cohen ~)-----------------
Alexander Li Cohen alexc@npg.wustl.edu (WORK Email) alexcohen@gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine
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