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Hi, Thank you for the response! I just sent a file via FTP:
freesurfer_aseg_edits_issue_example.zip
That zip file contains a directory structure with a deidentified example,
edited files, and outputs. It's a different example than the one in the image
but it should contain all the same steps. There are also a few text files with
details - INFO describes what is contained in each subfolder, COMMAND contains
the freeview command (loads up the final session where the fixes were undone
plus the original aparc+aseg.mgz and the previously corrected aparc+aseg.mgz),
and LOCATION contains a few example locations where the error is happening.
Let me know if there is any more information that would be useful to send along
or if I should send anything again in a different format. Thank you so much!
Sarah
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Monday, June 27, 2022 10:18 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aseg.presurf edits are undone or incomplete when
brainmask.mgz edits are involved
* External Email - Caution *
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Aaron Tanenbaum
<aaron.b.tanenb...@gmail.com><mailto:aaron.b.tanenb...@gmail.com>
Sent: Wednesday, June 22, 2022 3:52 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aseg.presurf edits are undone or incomplete when
brainmask.mgz edits are involved
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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<mailto: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<mailto: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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