External Email - Use Caution
and also, where can I find the documentation for the argument -atlas that the log proposed I should use? Couldn't find it anywhere...
On Wed, Sep 13, 2023 at 5:05 PM Rona Haker ronahannahh@mail.tau.ac.il wrote:
Thanks, I have already read this and tried to perform the instructions, but the files brainmask and the files under directory 'surf' have not yet been created so I cannot do it. Any other solutions?
On Sun, Sep 10, 2023 at 8:47 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
External Email - Use CautionIt looks like there is a huge defect which you will probably have to fix by hand if you want to use this case. See *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Y8S9-a_aN_4cgLVYzzMDZwmVbOKBrAKdYBb-6gjhmIB3m2... 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 CautionDear 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 brainBrain 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:
- 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 IDT2023
I would greatly appreciate some help!
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