Hi Edan
It’s hard for me to see what’s going on in those images. What is the intensity
of the white matter in the middle of the occipital strands in the brain.mgz and
the brain.finalsurfs.mgz? If it is significantly lower than 110 you probably
want some control points in the occipital lobe.
Cheers
Bruce
From: Edan Daniel <ed...@princeton.edu>
Sent: Friday, February 18, 2022 12:15 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Fischl, Bruce
<bfis...@mgh.harvard.edu>
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
External Email - Use Caution
Hi Bruce!
We are focusing on the occipital lobe where the white matter boundary is often
too far into the gray matter, and we need those voxels to record visual signals.
Attaching a few images for reference - notice how much 'thicker' the wm
segmentation is in the white.preaparc vs the lh.orig.nofix. wm edits of this
sort were accepted when we were using the same pipeline with v6 (separate
datasets), but now with v7 our edits get 're-corrected' and overwritten. We'd
be happy to provide more information or images.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Thu, Feb 17, 2022 at 7:01 PM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Edan
Sometimes control points can be more effective than editing the wm,
particularly if the intensities in that region are not what we expect (like if
the wm and gm are darker than what we try to set them to). Can you post an
image or two?
Cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Edan Daniel
Sent: Thursday, February 17, 2022 6:51 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
External Email - Use Caution
* Different data, same pipeline. In v6 our changes were included in the
final white surface segmentation, whereas in v7 they are overwritten during the
placement 'refining'.
* ?h.orig.nofix and ?h.orig DO reflect edits (?h.orig to some extent).
white.preaparc does NOT.
* We noticed that the placement is very stubborn and we were not able to
overcome this. Methods like manually editing the wm surface worked well with v6
and do not work now with v7. We have also tried editing the filled.mgz with
v7.2 following the new tutorial, and that did not work either.
Is there any way we can overcome this stubbornness?
Many thanks!
Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
The edits you are making only change the initial surface; the surface placement
then refines the placement. Sometimes the surface placement can be quite
stubborn. If this is the case, the ?h.orig.nofix and ?h.orig will reflect your
edits (nofix exactly; ?h.orig to some extent). Also check the the
white.preaparc is where the problem starts.
When you say that v6 did better, do you mean on this same data or on different
data? The surface placement has not changed that much since v6.
On 2/14/2022 12:50 PM, Edan Daniel wrote:
External Email - Use Caution
We have been having issues with recreating the final surfaces after editing the
white matter segmentation, which used to work smoothly in version 6.
After running a subject through recon-all (version 7.1.1 *without* the parallel
flag) and then editing the white matter, we run the following command (w
v7.1.1):
recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs '
num2str(corpus_point)
The ribbon file and surfaces do update *very slightly* but it’s largely
ignoring our (sometimes large) edits. This pipeline worked well for us in
version 6- do you have any idea what might be going on?
Would love to hear your thoughts about this.
Many thanks!!
Edan, Braindevlab@Princeton
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