Dear John, David,
To great summarization of David, I would add following:
My personal preference is to run whole -autorecon2 -autorecon3 after editing of
the brainmask.mgz.
Early stages of -autorecon2 (normalization, registration, volumetric labeling)
use brainmask.mgz, therefore I believe that their results can be improved when
improved brainmask.mgz is provided (especially when the edits of the
brainmask.mgz are of large extent).
When the pial surface extends to the cerebellum, different edits are needed as
specified here:
http://freesurfer.net/fswiki/FsTutorial/PialEdits_freeview
Antonin Skoch
Hi David,
Thank you for the feedback! I followed your advice's and everything has been
resolved. Highly appreciated!Cheers,
John
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-------- Original Message --------
Subject: Re: [Freesurfer] manual edits
Local Time: April 12, 2017 11:04 AM
UTC Time: April 12, 2017 3:04 PM
From: seman...@nyspi.columbia.edu
To: John Anderson <john.ande...@protonmail.com>, freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
Hi John,
Yes understanding how freesurfer deals with edits can be a bit confusing. I
have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross
sectional data in Freesurfer 5.3 so perhaps I can help.
Recon-all is basically a script which runs a series of about 25 or so
processing steps in a defined sequence. The software generally will be able to
recognize when an edit has been done at a particular intervention point and
will take those edits into account when running that step unless you
specifically instruct it not to.
The most common types of edits are edits to the wm.mgz to fix white matter
defects and tissue incorrectly identified as white matter, and edits to the
brainmask.mgz to fix cases where the skull strip is insufficient to prevent
dura and other non-cortical tissue from making it into the gray matter/pial
surfaces. White matter edits need to be done directly on the wm.mgz and gray
matter/skull strip edits need to be done on the brainmask.mgz. Editing those
two files and saving them directly in freeview is sufficient to register those
edits for recon-all.
If you have edited only the brainmask.mgz, it is sufficient to run
–autorecon-pial since the white matter surfaces will not need to be
regenerated. If you have edited the wm.mgz, you must run –autorecon2-wm (or
–autorecon2-cp if you used control points as well as white matter edits). If
you have edited both the brainmask.mgz and the wm.mgz, then you only need to
run –autorecon2-wm since the pial surfaces will be regenerated taking into
account the brainmask.mgz edits as part of that workflow. Keep in mind that you
still need to run –autorecon3 to complete the reprocessing of these data
(-autorecon-pial includes the steps from –autorecon3) but that can be done when
you are happy with your final surfaces if you want to save processing time on
iterative edits.
Here is the wiki page referring to edits:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
I hope this is helpful.
Best,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
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From: John Anderson <john.ande...@protonmail.com>
Reply-To: John Anderson <john.ande...@protonmail.com>
Date: Wednesday, April 12, 2017 at 6:45 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] manual edits
Dear Freesurfer experts,
I am not an expert in manual edits, so I highly appreciate any feedback
regarding the issues in my questions below. I ran the following command line
“recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing
the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached.
Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz"
1. When I reviewed “wm.mgz” I see interactions between the white matter (wm),
and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the
wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz”
2. I found many holes in many slices similar to the (black arrow). I filled all
these holes. The data saved in “wm.seg.mgz”
3. I fixed some issues related to dura and bad skullstipping
Then I ran the command:
“recon-all -autorecon2-wm -autorecon3 -subjid <subject>” which output the file
“brain.finalsurfs.mgz”
and the command
“recon-all -autorecon-pial -subjid <subject>”
Now, I want to understand where Freesurfer implement the new edits? Which files
will be used as the main files that include the new edits. Logically, the edits
must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I
open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original
non-edited files. I am not sure what I am doing wrong so I highly appreciate
any help.
John
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