Dear David,
thank you for the feedback; I saw your posts concerning edits and responded to them, see
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html
Just my case is not concerning poor response to the edits (which I believe is not systematically different between 5.3 and 6.0), my concern is that the data processed by v6.0 need much more wm.mgz edits than data processed by v5.3.
I think that my issue lies in -normalization2 step of recon-all. One of the difference between v5.3 and v6.0 is that by default the -mprage flag is passed to mri_normalize. This affects several parameters inside mri_normalize. I tried to reprocess my subjects using v6.0 with -no-mprage, but unfortunately this did not help.
See the example screenshots processed by v5.3 and v6.0 with -no-mprage:
The brain.mgz is still more aggressively filtered in v6.0 and there is much more prominent leak of ?h.white outside brain, which is probably caused by extended filtration which affects GM/WM contrast.
Looking at the source code of mri_normalize.c I did not comprehend where the basis of the issue lies, but in any case there are big differences in mri_normalize.c code between versions.
Antonin
From: David Semanek SemanekD@nyspi.columbia.edu To: Antonin Skoch ansk@ikem.cz, "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: 4/20/2017 3:41 PM Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
Agreed. A validated protocol run on a very large group of subjects in 5.3 was attempted with similar data in 6.0 and not only was the longitudinal edit stream nearly non-functional for white matter edits, cross edit performance was disappointing. I am currently waiting on a response to these potential issues before pursuing further work with 6.0. Best,
David P. Semanek, HCISPP Research Technician, Posner Lab Division of Child and Adolescent Psychiatry Columbia University Medical Center New York State Psychiatric Institute 1051 Riverside Drive, Pardes Bldg. Rm. 2424 New York, NY 10032 PH: (646) 774-5885 IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
From: Antonin Skoch ansk@ikem.cz Date: Wednesday, April 19, 2017 at 5:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
Dear experts,
I am sending just one more example to illustrate issue with white surface estimation in v6.0. See the attached screenshots: In v6.0 there seems to be insufficient contrast in brain.finalsurfs.mgz, so the white surface is leaking at three spots dramatically outwards towards pial surface. The white surface in v5.3 looks much more anatomically relevant in the same spot.
Could you please comment on how to avoid such issues in v.6.0?
Regards,
Antonin Skoch
