if you send us a volume we'll take a look. Basically Randy's mp-rage had significantly darker gray matter than we were used to in SPGR and MPRAGE images. If wm was around 110, I think typical GM is around 75, but Randy's were around 60.
cheers, Bruce
On Wed, 26 Aug 2009, Alexander Li Cohen wrote:
Ah I see, this raises a question then, of whether the optimizations are still applicable to WU acquired MP-RAGE data, as we are currently collecting 3T Trio data, and I believe Randy's data is 1.5T Vision data, however the sequence (our CAP MP-RAGE) is quite similar... can anyone up there speak to this?
-Alex ~)-------------
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
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.
On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote:
yes, it was optimized for the mp-rages that Randy B used to collect there, not for example ADNI. On Tue, 25 Aug 2009, Michael Harms wrote:
I assume that that flag (-washu_mprage) is somewhat antiquated, right? That is, it was included for an older set of scans (generated at WashU generated years ago before Siemens had its own MPRAGE sequence) that happened to have darker gray matter, and doesn't need to be applied for "modern" MPRAGE scans, correct?
-MH
On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote:
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer