Dear Free Surfer developers,

I have several subjects that are not successful with recon-all. In most cases, the log file looks something like the one attached, with errors in "inflating to sphere" and in "validation":

*********************VALIDATION*********************
curvature mean = -0.010, std = 0.009
curvature mean = 84.153, std = 7.183

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
before rotation: sse = 11.66, sigma = 23.42
after rotation: sse = 11.66, sigma = 23.42
Localization of inacurate regions: Erosion-Dilation steps
the sse mean is 19.34, its var is 27.07
before Erosion-Dilatation 24.37% of inacurate vertices
after Erosion-Dilatation 37.82% of inacurate vertices
58.52% of 'positive' inacurate vertices
41.48% of 'negative' inacurate vertices

The surface validation has detected a possible Error
If the final segmentation is not valid,
try using the option '-atlas'

Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...40 iterations

mri_strip_skull: done peeling brain

Brain Size = 2625362 voxels, voxel volume = 1.000 mm3
= 2625362 mmm3 = 2625.362 cm3

the /mri output directory is missing aparc+aseg and looks like this:

I tried running the recon-all command with the option '-atlas' as suggested in the log with this command:

export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=<path_to_subject>
cd $SUBJECTS_DIR

recon-all -s 00_FSseg -i 8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all -atlas

but:

1. I could not find any documentation on this option, what it means and what arguments to give it.

2. I get the following error:

'ERROR: Flag -atlas unrecognized.

-s 00_FSseg -i 8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all -atlas
Linux nbelab 4.15.0-206-generic #217-Ubuntu SMP Fri Feb 3 19:10:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 00_FSseg exited with ERRORS at Mon Sep 4 17:02:23 IDT 2023

I would greatly appreciate some help!