Doug,

        did you process from scratch or did you retain edits to
        brainmask.mgz and wm.mgz?

        The -cubic should not be necessary, since recon-all (which I
        primarily obtained from
        https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
        has UseCubic=1 ).

        I could try to replicate v5.3 again on my side.

        Antonin

        It is subject #1, trying to replicate in our version of 5.3
        using the 
scripts/recon-all.local-copy

./recon-all.local-copy -all -FLAIRpial -s 1.dng.v53.local-cubic -cubic
The results were close, but they were not exact

On 5/1/17 4:13 PM, Antonin Skoch wrote:

Dear Doug,

that is strange. What precisely you cannot replicate? The results with v5.3 or 
with v6.0? What subject from the group I uploaded you have tried?
I could try to run the comparison again but I have seen the results already in 
many subjects and the difference between -cubic and no cubic seems profound and 
systematic in favor of v5.3 in the aspect of wm.mgz leak ouside brain and GM/WM 
contrast.

Concerning the expert options file: Despite using flag -xopts-use in recon-all 
in v5.3, I did not use any expert option file in
the subject I have uploaded. The reason of using -xopts-use was that I was 
processing the subjects in batch where some of them had expert-options file 
with entry bbregister -init-header due to the fact that init-fsl failed in 
these subjects.
I wanted to make my life easier by processing all of them by identical 
recon-all command line parameters and added -xopts-use to all subjects (even in 
the subjects without expert option file). I supposed that this could not do any 
harm.

Antonin

I can't seem to replicate your results locally, even with the recon-all
you used. The one thing I'm missing is the expert options file. Can you
send that to me?
On 04/24/2017 12:49 PM, Antonin Skoch wrote:
> Dear Doug,
>
> the subject with leak of white surface outside brain (my first post with
> screenshots) is subject 1. Slice number (coronal) around 100.
> The subject in second post (with text below) is subject 2, slice number
> (coronal) also 100.
>
> I have processed the subjects with v 6.0 (in fact dev version from feb 2017,
> but this is irrelevant) with -cubic -no-mprage. It looks much like v5.3, i.e.
> the wm.mgz and surfaces are much better, but v5.3 looks still better, at
> least for subject 1.
> I have uploaded them as file v6.0_cubic_no_mprage.tar.gz to your ftp site.
>
> The optical difference in norm.mgz/brain.mgz between v5.3 and v6.0 with
> -cubic is very minor, but still there is some other thing which renders
> wm.mgz worse than with v5.3 for subject 1.
> The -cubic has profound effect, the images seem much smooth with lose of
> contrast without using -cubic.
>
> Regards,
>
> Antonin
>
>
> 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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