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Hello FreeSurfer Developers and Community,

I am currently refining surface reconstructions for my subjects by performing manual edits on both the white matter segmentation and pial surfaces using FreeSurfer.

According to the FreeSurfer documentation, after making white matter edits, the recommended command is:
 
  recon-all -autorecon2-wm -subjid <subject>
 
and after pial surface edits, it is recommended to run:

  recon-all -autorecon-pial -subjid <subject>
 
followed by:

  recon-all -autorecon3 -subjid <subject>

My main goal is to ensure that both white matter and pial manual edits are correctly incorporated without losing either.

However, I have seen in the FreeSurfer tutorial the combined command:

  recon-all -autorecon2-wm -autorecon3 -subjid <subject>

which runs both stages sequentially.

I have two related questions:

1. If I run `recon-all -autorecon2-wm -autorecon3` after both white matter and pial edits, will my manual pial edits be preserved, or will they be overwritten by the `-autorecon2-wm` step?

2. Is the recommended workflow to run `-autorecon2-wm` first, then `-autorecon-pial` as a separate command, and finally `-autorecon3`? Or can some of these stages be combined safely in a single command line?

For reference, I am using:
- FreeSurfer version: 7.4.1
- Platform: Red Hat Enterprise Linux

With gratitude,

Camilo

===================================

Camilo Castelblanco Riveros (He/His)

Neuroscience Ph.D. Candidate (G4)           

Robertson Lab & Bujarski Lab

Student Interest Group in Neurology (SIGN) Co-Leader

Global Health Fellow

e: ccastelblanco.gr@dartmouth.edu

Zoom

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