edu>
*Sent:* Monday, February 21, 2022 11:14 AM
*To:* Fischl, Bruce
<mailto:bfis...@mgh.harvard.edu>
*Cc:* Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in
white matter segmenta
t;
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Edan Daniel
> *Sent:* Monday, February 21, 2022 6:30 PM
> *To:* Freesurfer support list ; Greve,
> Douglas N.,Ph.D.
> *Subject:* Re: [Freesurfer] autorecon2-wm not refl
: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
External Email - Use Caution
Hi Doug,
It is something we do *a lot* of, thus we hoped we'd be able to find a way to
make the recon-wm implement our edits without additional manual edits
ns)
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* Edan Daniel
> *Sent:* Monday, February 21, 2022 11:14 AM
> *To:* Fischl, Bruce
> *Cc:* Freesurfer support list
>
> *Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in white
> matter segmentat
21, 2022 11:14 AM
*To:* Fischl, Bruce
*Cc:* Freesurfer support list
*Subject:* Re: [Freesurfer] autorecon2-wm not reflecting edits in
white matter segmentation (7.1.1, 7.2.0)
*External Email - Use Caution *
Thanks Bruce!
This looks like a helpful solution for the places where the wm
..@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 nee
.
Cheers
Bruce
From: Edan Daniel
Sent: Friday, February 18, 2022 12:15 AM
To: Freesurfer support list ; Fischl, Bruce
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
...@nmr.mgh.harvard.edu
On Behalf Of Edan Daniel
Sent: Thursday, February 17, 2022 6:51 PM
To: Freesurfer support list
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
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
External Email - Use Caution
Hi there,
Here's an issue that keeps coming up:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
source: no such file or directory: /Applications/freesurfer
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
-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Thursday, February 17, 2022 6:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] autorecon2-wm not reflecting edits in white matter
segmentation (7.1.1, 7.2.0)
The edits you are making only change the initial
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
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
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