External Email - Use Caution
It looks like there is a huge defect which you will probably have to
fix by hand if you want to use this case. See
https://secure-web.cisco.com/1AMkvq3aFvAxz7-H1y5F071f2fyGqYpXaIOw7V46NLOVrr8agLP0RsNfxinekhl4cL34_t-ZzSoffLkqFmj8F-0OUuxklCU9ixROLbS5JUID7ZsLA4kbFNudqpg7dFPXlIDMqf6StF7q7lpNxQ1q84UcWkFeaWLmtXwHejUh-fR9fpE9HPWyQh1Hdkw0C8qEbvmGyWCJ9aMMAhAHiPukgZO6wbjF3Od71wKasMz7D7p5Ln0CyD6QrvbZrifBPHDiJuJZetRi042UrvhhuneV8xQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview
On 9/4/2023 10:13 AM, Rona Haker wrote:
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.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!
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