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: SemanekD@nyspi.columbia.edu To: John Anderson John.anderso@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.anderso@protonmail.com Reply-To: John Anderson John.anderso@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