External Email - Use Caution
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: [image: image.png] 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!
