answers below
On 11/4/2025 8:19 AM, Camilo Castelblanco Riveros wrote:
External Email - Use Caution
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:
- 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?
They will be preserved.
- 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?
You can safely combine them as in #1 above. You can add -autorecon-pial to #1 if you want, but it should not matter.
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 https://secure-web.cisco.com/1VGQeQdcjwLtBi3C9UBo55c7SqVai-UrjQm1lF9QaAVlL0oK7sskyT2Fb3fd82rUgYGwY_PCggJChMV7pfIIpAzJYWFoiAqgsUv46AgWxg1ull5IaIlwkfl0ZZsatPrr-hWW5tpg8SPdUuCli-18NUR56FdQ057ba4n1_NY0uUsGyyIVmEfrRFUtT6VWQK7ZZLJr84RM5k9zNq6_mZMpLOPOZ1LM79lcNyH2N1M1r82UTQB35nLEjauuEAtUhrQuZrLYwPtJjAVuaKFZ93oOY_fl9hWpMLgXZ5KLN4VhZ6w3MFs19ggMn6vB3LnZD4GDTeRPo4hHyGqf7qBjX5cSTjw/https%3A%2F%2Fwww.robertsonlab.com%2F & Bujarski Lab https://secure-web.cisco.com/1y_9Zgr30ubJ5JlJFc0I6-yJcgPm8sSkph5TvzTpqhl6nvOdHpRsdvXtFo1zZs3sQmjgsRpsIxcw6aDIrT_zAaxjliq5lmo1xwYq9P4UWjkILmT_inJBvp0iVQS49vq9nD64PN6RlsouCSVVFh3ljI2enwwAEqHtjmKWwA7ebd_O1KG5kLb---4KonhWeDflpFmkRgVNrF3ssVzr2AznSkUJJhkYA25r4ZtI87UEoE3WRlzzidVEel8HpYnmBBFFDEKMfBOxtSB3jslcrLWQWmd6eMs0_QS1K0_Ebq4c71vdYMKa9U_m-3i3r2_Y89iUMJLUfMzRLtfqAa0VsiZOZfQ/https%3A%2F%2Fwww.dartmouth-hitchcock.org%2Fresearch%2Fsearch-clinical-trials%2Ftrial%2FSTUDY02001606
Student Interest Group in Neurology (SIGN https://secure-web.cisco.com/1uGgfMp5acPV-NG-koj4ZIyk0_wqPKAvcoF_BCuwGLKcw_qtEMxXEcxJtSDUvIxXducllRYSz4WhVhGCviEySSr5o6V0wO3Hp0cihft55vhv3WVZsWNVtQX2cXkoYvnS4K7U5kPCol4vZK2G5pkLeYV59_X0bk1glQYgj8N5kOsIJSgZ4_Dcp0bD7uP-i6lcjo2Rxa3BwQhIHFuelX2P5fsol9VcqnrnlPhDrbHj5LWOBHFD4n6gVGKD06M-7XRXhVAcpZZL1YiXTrqyOZa_L2gaaS8k9QvCCNX58hDHDPa19VGBARvxqCKPohOKoOlhPlYwj6OlXFjVQNMLAEBiV5Q/https%3A%2F%2Fgeiselmed.dartmouth.edu%2Fstudent-gov%2Fstudent-groups%2F) Co-Leader__
Global Health Fellow
e: ccastelblanco.gr@dartmouth.edu
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