right, but it is not affecting the subcortical structures (eg, compare
to aseg.presurf.mgz)
On 3/31/2023 1:14 PM, Keefe, Sarah wrote:
External Email - Use Caution
It's definitely affecting segmentation in the aseg.mgz, as well as the
aparc+aseg.mgz which is what we usually use. Screenshots attached
(FreeSurfer 7.3.2, "-all -qcache", no editing performed yet). It's
over-labelling orbitofrontal here which we see a lot with these. We
also see it affecting insula, accumbens, and putamen labeling. I
wouldn't be concerned if it wasn't so biased toward the right
hemisphere every time. We haven't seen it happen on the left yet.
The 255 voxels on brain.finalsurfs.manedit.mgz helped things somewhat
but at this point the 5.3 results with no edits are still looking
consistently better in this area.
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Friday, March 31, 2023 8:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] White matter exclusions occurring in
v7.3.2 but not v5.3
** External Email - Caution **
oh, it won't have any impact on the subcortical volumes. Those are
measured without reference to the surface. Or are you seeing something
that looks funny? Look at the subcorts in aseg.mgz.
On 3/31/2023 8:22 AM, Dierker, Donna wrote:
External Email - Use Caution
Hi Doug,
Understood, but it is strange that we are seeing this only in the rh.
In 25 sessions (albeit a third fairly minor).
We are less concerned about thickness in this region than impact on
subcortical volumes.
We realize this probably can’t be fixed, but we wanted you to be
aware of it.
Thanks,
Donna
*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 Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Date: *Wednesday, March 29, 2023 at 8:58 AM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] White matter exclusions occurring in
v7.3.2 but not v5.3
** External Email - Caution **
Frm an automated standpoint, there is not much more to do. That area
may be part of the medial wall anyway. If you want to fix it
manually, you will have to
cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
Then edit the manedit in freeview to fill in those regions with 255
Then rerun recon-all -s subject -autorecon-pial ( this will do white
and pial)
On 3/27/2023 6:32 PM, Keefe, Sarah wrote:
* External Email - Use Caution *
Thank you! That does describe the problem. I tested that out and
it just completed and unfortunately that adjustment didn't change
things significantly from the original run. A screenshot is
attached. I made very very VERY sure that the recon-all log for
the right side screenshot did really incorporate the xopts file,
and that the WhitePreAparc call had that flag included correctly.
The output on the right side of this screenshot is 100%
definitely using the custom xopts file and in the recon-all.log
it correctly added the --rip-bg-no-annot flag to WhitePreAparc.
Any chance you have other suggestions in this vein?
Happy to send these output subject directories if needed.
Thanks again,
Sarah
------------------------------------------------------------------------
*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
Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, March 27, 2023 10:06 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] White matter exclusions occurring in
v7.3.2 but not v5.3
** External Email - Caution **
Does this describe the problem?
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Bug fix: improve surface placement in inferior frontal area near
putamen. There are some cases where the white surface is not
placed well in these areas because of the close proximity of
putamen to cortex; it is probably the case that the surface is
not well-defined in this region anyway, but the placement can be
improved by creating an expert options file with the line
"WhitePreAparc --rip-bg-no-annot"
Let me know if that fixes the problem
On 3/22/2023 5:00 PM, Keefe, Sarah wrote:
* External Email - Use Caution *
Hi FreeSurfer Team,
Our group is working on reprocessing scans that we originally
processed (performed quality control and edited where
necessary) with FreeSurfer 5.3 with the HCP patch. We are
aiming to reprocess everything with FreeSurfer version 7.3.2.
So far when checking and editing FreeSurfer 7 outputs we're
regularly seeing areas of brain that should be included
within the white matter surface but are not, particularly in
the accumbens and orbitofrontal areas. The areas are of lower
intensity within the scans, but FreeSurfer 5.3 is able to
handle these areas accurately - we don't see these issues in
our runs on the same scan files done in FreeSurfer 5.3.
I've attached a screenshot of the Freesurfer output of each
version side by side on one of the slices where the exclusion
is happening. We're seeing this on maybe 1 in 10 Freesurfer 7
scans. All did fine in 5.3. We're finding that the problem is
not limited to certain scanners - one of these examples is
from a Biograph PETMR scan and the other is from a Prisma.
Is there a recommended flag or flags we could use with
Freesurfer 7 recon-all that might get us closer to the way
5.3 handles this?
The Freesurfer 5.3 parameters we originally used were:
-all -qcache -hippo-subfields -nocubic -mprage
The Freesurfer 7.3.2 parameters we are using now are:
-all -qcache
I have the recon-all outputs of both versions and the
original scan available and can send them via FTP if that
would be helpful.
Other notes: Running with the -mprage flag added to the
Freesurfer 7.3.2 recon-all launch was not different from the
FS 7.3.2 recon-all launch without the flag but I can send
that output along as well if it would be useful. Also, these
examples are done in 7.3.2 but we've also run into this issue
with 7.1.1.
Really appreciate any assistance you can provide, as trying
to figure this out has been delaying our processing a bit.
Thanks so much,
Sarah
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