Can you send us the data? Just one case with a copy of the original data
and a copy of the data where you reran recon-all but it did not protect
the edits. Also, send a freeview command line that will load up the two
volumes and the col, row, slice of a location where there were edits in
the first but not in the second. The idea here is that I won't have to
go on a snipe hunt for the problem. Every couple of years, someone posts
this type of problem, but I've never been able to track it down.
On 6/27/2022 11:00 AM, Keefe, Sarah wrote:
External Email - Use Caution
Hi, just wanted to follow up on this and see if anyone on the
Freesurfer team has any thoughts or suggestions on how to solve this.
Thanks so much!
Sarah
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Aaron Tanenbaum
<aaron.b.tanenb...@gmail.com>
*Sent:* Wednesday, June 22, 2022 3:52 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] aseg.presurf edits are undone or
incomplete when brainmask.mgz edits are involved
** External Email - Caution **
External Email - Use Caution
Correction, not cerebellum inclusions but dural inclusion being
labeled as cerebellum. When editing I am setting these dural inclusion
as 0 in the brainmask, i am using -autorecon2 flag, and I never edit
more then one image before rerunning recon-all.
On Wed, Jun 22, 2022, 9:23 AM Aaron Tanenbaum
<aaron.b.tanenb...@gmail.com> wrote:
So I believe I posted something like this a while ago. My
observation is that edits removing voxel from the brain mask does
not always remove inclusions for the cerebellum. It seem to work
for the rest of the brain. I find this to be a common occurrence.
On Thu, Jun 16, 2022, 7:02 PM Keefe, Sarah <sarahke...@wustl.edu>
wrote:
External Email - Use Caution
Hi FreeSurfer Team,
Our group is in the process of switching to Freesurfer 7.1.1
from 5.3. We have been taking advantage of Freesurfer 7's
aseg.presurf volume to add in correction of unlabeled
cerebellum to our standard edit checklist rather than our
previous workflow of having a Freesurfer fail our quality
control standards and be excluded from analysis if too much
cerebellum is unlabeled on aparc+aseg segmentation. We're
consistently running into an issue when we have a Freesurfer
that requires corrections to both brainmask.mgz and
aseg.presurf.mgz.
An example of when this happens is if the Freesurfer output
labels dura as cerebellum cortex on aparc+aseg (which requires
erasing the included dura from brainmask.mgz) and the output
also has an exclusion of cerebellum from the aparc+aseg
segmentation (which requires correctly labeling the excluded
voxels on aseg.presurf.mgz). We have found that if we edit
both the aseg.presurf.mgz and brainmask.mgz volumes and then
rerun recon-all with both, the cerebellum exclusion
segmentation fix does not "take" completely and individual
voxels in the cerebellum that were corrected in the edited
volume are still left unlabeled. We have 100% confirmed that
our labeling edits to aseg.presurf are correct and complete
before this happens. To reduce confusion and attempt some
consistency across our editing team, we relaunch recon-all
with the same flags every time: -autorecon2 -autorecon3 -qcache
To work around this issue, we implemented a workflow where
editors will make brainmask.mgz corrections, then rerun
recon-all (rerun 1), and then make aseg.presurf corrections,
and rerun recon-all again (rerun 2). This seems to work
although it is frustrating since we are trying to minimize the
number of reruns of recon-all and we typically tell people to
stop and make a final quality control decision after 3 reruns.
What we are finding is if another issue pops up on
brainmask.mgz after rerun 2 that then needs corrections (e.g.
other areas of dura are incorrectly included in the pial
surface or aparc+aseg cerebellum labeling but weren't included
before so weren't erased) then after making those edits and
rerunning recon-all, the previously corrected aparc+aseg
cerebellum segmentation shows "missing" unlabeled voxels, same
as if we had run recon-all once with both aseg.presurf and
brainmask volumes edited.
The attached image shows an example of our process and the
issues we're seeing. The end result (F) also happens if we
edit both brainmask.mgz and aseg.presurf.mgz edits and rerun
recon-all once with both included.
screenshot A is the aparc+aseg.mgz of the original recon-all
output (run 0) where cerebellum is unlabeled (red arrows).
There is also visible dura labeled as cerebellum that we need
to fix (yellow arrow).
screenshot B is the aparc+aseg.mgz of the recon-all rerun
output after just the brainmask.mgz was edited and saved (run
1). Additional segmentation issues have appeared in addition
to the original ones (red arrows). This screenshot also shows
an example of the type of edit we are doing to brainmask - we
have erased dura from brainmask.mgz to correct the cerebellum
cortex labeling and the edit worked (yellow arrow).
screenshot C is the aseg.presurf.mgz volume after run 1 before
editing for the cerebellum exclusion issue.
screenshot D is our edited and saved aseg.presurf volume
BEFORE we run the second recon-all relaunch. We have corrected
the labeling (green arrows).
screenshot E is the aparc+aseg.mgz after a recon-all relaunch
with only the new edit to aseg.presurf. (run 2). The
cerebellum exclusion error has been fixed in aparc+aseg (green
arrows). This run 2 of recon-all caused more issues to show up
that required more brainmask.mgz edits.
screenshot F is what we see if we edit brainmask.mgz again and
rerun recon-all (run 3). The output of run 3 shows missing
voxels in the cerebellum where we had fixed them before.
Unlabeled voxels appear throughout the areas that were edited
in C and were corrected in D.
We try to minimize edits and maintain consistency across our
editing team by asking people to only erase dura from
brainmask.mgz that has been erroneously included in the
cerebellum labelling or in the pial surface (rather than other
dura that also happens to be included in the brainmask.mgz).
We also ask people to relaunch recon-all with the same
-autorecon2 -autorecon3 -qcache flags each time for
consistency across our data. We really really want to be able
to cut down the number of times we are relaunching recon-all
but we are unable to fix both these issues at once (it ends up
like screenshot F after 1 rerun).
Is there a way to prevent the aseg.presurf.mgz edits from
"undoing" voxels when brainmask.mgz edits are included or done
after aseg.presurf? Any assistance or alternative techniques
for solving this would be much appreciated.
We are primarily using the Freesurfer 7.1.1 Docker container
but I have also been able to replicate this issue on CentOS 8
and Ubuntu 20.04 with build stamp
freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551.
Thanks so much,
Sarah
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