Thank you for looking into the deeper mechanics of this issue. In my case I am dealing with motion contaminated 1.5T data which require extensive and somewhat intricate edits to the white matter bleed into the pial surface, as well as into dura. In working with a past dataset of similar characteristics I was consistently impressed with fs 5.3’s ability to properly segment white matter in most cases and the robustness of the editing response. I was left with the overall impression that freesurfer handled noisy data quite well with a little bit of help. Our results from the analysis of corrected vs uncorrected data were very strong in favor of the editing protocol.

My experience with 6.0, aside from any issues of information not propagating through the longitudinal stream, is that there are many more cases in which the white matter surface will not conform to the edits suggested in the white matter volume. A number of tricks to “convince” the software in cases of non-response used in 5.3, such as making sure to complete edits on adjacent slices, are simply not effective. I am left with the overall impression that I have very little control over the white matter surfaces really, beyond making suggestions which may only slightly change the degree of error, but does not fundamentally change the structure of the white matter surface enough to remove the misclassification entirely in many cases.

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: Thursday, April 20, 2017 at 10:25 AM To: David Semanek SemanekD@nyspi.columbia.edu, "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

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

Thanks Bruce I’ll prepare something and upload it, hopefully before the weekend. I’ll let you know when I’ve got it uploaded.

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.

On 4/20/17, 11:14 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi David

I can take a look at a subject of yours as well if you upload it (both 5.3 and 6.0 processed versions if you have them) and point me at voxel coords. The white surface is by design insensitive to local variations which is what makes it robust, but also makes it more difficult to modify. I'll take a look and think about how to make it easier

cheers Bruce

On Thu, 20 Apr 2017, David Semanek wrote:

> > Thank you for looking into the deeper mechanics of this issue. In my case I > am dealing with motion contaminated 1.5T data which require extensive and > somewhat intricate edits to the white matter bleed into the pial surface, as > well as into dura. In working with a past dataset of similar characteristics > I was consistently impressed with fs 5.3’s ability to properly segment white > matter in most cases and the robustness of the editing response. I was left > with the overall impression that freesurfer handled noisy data quite well > with a little bit of help. Our results from the analysis of corrected vs > uncorrected data were very strong in favor of the editing protocol. > > > > My experience with 6.0, aside from any issues of information not propagating > through the longitudinal stream, is that there are many more cases in which > the white matter surface will not conform to the edits suggested in the > white matter volume. A number of tricks to “convince” the software in cases > of non-response used in 5.3, such as making sure to complete edits on > adjacent slices, are simply not effective. I am left with the overall > impression that I have very little control over the white matter surfaces > really, beyond making suggestions which may only slightly change the degree > of error, but does not fundamentally change the structure of the white > matter surface enough to remove the misclassification entirely in many > cases. > > > > 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: Thursday, April 20, 2017 at 10:25 AM > To: David Semanek SemanekD@nyspi.columbia.edu, > "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in > comparison to v5.3 - worse GM/WM contrast > > > > 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 > > >

And what slice number?

On 04/24/2017 11:16 AM, Douglas N Greve wrote:

Anonin, of the three subjects you sent, which one is shown in these pictures?

On 04/19/2017 05:23 PM, Antonin Skoch wrote:

...

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

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