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Hi Jackson,
Thank you for the reply!
I appreciate the explanation. It makes sense the wm.mgz edits need to be run before the brainmask.mgz edits through the recon-all pipeline. Just to clarify, would it be preferred to run:
“recon-all –s subject –autorecon2 –autorecon3” or “recon-all –s subject –autorecon2-wm –autorecon3”
when running both the wm.mgz edits and brainmask.mgz edits through the recon-all pipeline?
Both –autorecon2 and autorecon2-wm flags run the the wm steps first followed by the pial surface steps. However, since the –autorecon2 flag starts at an earlier step in the pipeline (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Manual-InterventionWorkflowDirectives), would there be a chance it would ignore/erase any of the manual edits done?
Thank you in advance for the clarification!
Aylin
Aylin Dincer
aylin.dincer@wustl.edu
From: Nolan, Jackson [mailto:JNOLAN5@mgh.harvard.edu]
Sent: Wednesday, January 13, 2021 10:31 AM
To: freesurfer@nmr.mgh.harvard.edu; Dincer, Aylin <aylin.dincer@wustl.edu>
Subject: Re: freesurfer flag for multiple edited volumes
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Greetings Aylin,
If you have made edits to both the brainmask.mgz and wm.mgz files, I would recommend running recon-all with the -autorecon2 and -autorecon3 flags.
Each step in the FreeSurfer recon-all process draws on files generated in previous steps. So, if you have made edits to the wm.mgz volume, you will need to re-run the portion of the recon-all pipeline to incoperate you wm.mgz edits before you run the edits you made to brainmask.mgz through recon-all. This is because the pial surface processing happens after the white matter segmentation.
Below is a link to the FreeSurfer wiki page about recon-all. The section "Manual Intervention Workflow Directives" gives a breakdown of the steps in the recon-all pipeline.
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Description. Performs all, or any part of, the FreeSurfer cortical reconstruction process. This help only gives some simple information. See also ReconAllDevTable.. Basic usages: 1. Subject dir does not exist: surfer.nmr.mgh.harvard.edu |
Best,
Jackson
From:
freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
on behalf of Dincer, Aylin <aylin.dincer@wustl.edu>
Sent: Wednesday, January 6, 2021 1:05 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] freesurfer flag for multiple edited volumes
External Email - Use Caution
Hello FreeSurfer Experts,
If I need to manually edit both the brainmask.mgz and the wm.mgz in a FreeSurfer, what are the recommended flags when rerunning recon-all with the edits (-all, -autorecon2, etc)? Or is it recommended to run an edited volume through recon-all one at a time (i.e. editing the brainmask.mgz first, running recon-all using autorecon2-pial flag, editing the wm.mgz afterwards, then running recon-all again with autorecon2-wm)?
Thank you for the help!
Aylin
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