Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast
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
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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Douglas N Greve