Dear Bruce, sorry for the confusion with xopts-use and recon-all editing.
I have checked the xopts-use and the reason of this is that I run the subject 1 and 2 as a part of batch job on large amount of subjects, where I rerun recon-all to anonymize them. Some of them had expert-options file with bbregister --init-header from the initial run (these were subjects where --init-fsl failed). I put -xopts-use to invocation of all subjects (even for them without expert-option file) to make my life easier. I did not put -cubic expert-options to any of my subjects. Concerning editing of my 5.3 version of recon-all: My only modification in recon-all was -nsigma_above 8 for FLAIRpial and patch with .touch files recommended here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41284.html Otherwise my recon-all corresponds to the 5.3.0-patch version. It seems that there was change in UseCubic wich 5.3.0-patch. Original recon-all from 5.3.0 has UseCubic=0, whereas recon-all from 5.3.0-patch has UseCubic=1: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/recon-all In my v6.0 recon-all I have UseCubic=0. I am surprised that mere interpolation could have such profound effect ! I will try your suggestions and let you know. Antonin From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> To: Antonin Skoch <a...@ikem.cz> Cc: <freesurfer@nmr.mgh.harvard.edu> Sent: 4/21/2017 1:00 AM Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast Hi Antonin Doug points out to me that you edited your copy of recon-all in 5.3, which makes it really hard for me to track down any differences. For sure your recon-all used cubic interpolation for conforming by default, which introduces pretty big differences right at the start that I expect explain the majority of the differences in wm positioning that you are seeing. I guess I would suggest trying 6.0 with cubic on (-cubic) and see if they become more similar cheers Bruce On Thu, 20 Apr 2017, Antonin Skoch wrote: > > Dear Bruce, > I am uploading 3 example subjects processed both by v5.3 and v6.0 I referred > to in the screenshots in my previous posts: > Subj 1 - large leak of white surface outside brain in v6.0, not present in v > 5.3. RAS coords -53,-1,75 > Subj 2 - another measurement of identical subject - white surface is leaking > at three spots dramatically outwards > towards pial surface in v6.0. RAS coords -48,-2,64 > Subj 3 - leak of white surface outside brain. Both v5.3 and v6.0 has error i > n white surface, but the error is much larger in v6.0. RAS coords 48,5,78 > The v6.0 version is without removing -mprage. Removing -mprage in v6.0 cause > d only very small change in brain.mgz, the filtering is still much higher th > an in v5.3 and still causes the white matter surface leak. > The subjects are in files mri_normalize_v5.3.tar.gz and mri_normalize_v6.0.t > ar.gz. > I would very welcome any suggestions how to: > 1. Prevent new white surface errors in v6.0 in subjects previously processed > and edited by v5.3 > 2. How to make edits to modify white/pial surface location where wm.mgz edit > ing is not sufficient. > I tried workaround of directly editing 001.mgz as I discussed in thread http > ://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html > This is very time consuming. > Better way is maybe to consider implementation of option for mris_make_surfa > ces similar to -overlay option for cases where wm.mgz voxels have value 1 as > I discussed here: > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52730.html > Antonin > Hi Antonin > > yes, the -mprage flag is likely to be at least one source of the > differences. It makes the normalization more aggressive (since mprage trades > higher CNR for lower SNR). I'm surprised removing it didn't help. I think > that changing things like wlo could also help depending on how wrong the > normalization is. Upload a subject and I'll take a look > > cheers > Bruce > > > On Thu, 20 Apr 2017, Antonin Skoch wrote: > > 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 <seman...@nyspi.columbia.edu> > To: Antonin Skoch <a...@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 <a...@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 > > > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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