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 > al...@npg.wustl.edu (WORK Email) > alexco...@gmail.com (Non-secure / rapid-response Email) > Petersen/Schlaggar Lab > Medical Scientist Training Program > Washington University in St. Louis School of Medicine > ---------------------------------------------------------------------- > > This message is intended only for the exclusive use of the intended > recipient(s) named herein and may contain information that is > PRIVILEGED and/or > CONFIDENTIAL. If you are not the intended recipient, you are hereby > notified > that any use, dissemination, disclosure or copying of this > communication is > strictly prohibited. If you have received this communication in > error, please > destroy all copies of this message and its attachments and notify us > immediately. > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
