External Email - Use Caution 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 <dgr...@mgh.harvard.edu> wrote: > 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 *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1UVSh_UmU1Wz20AM-PQaf5ZsoYDlMuERL3xt9vJi1A70CBoVYOutAxVDfvmoCJEkyNk8bvm2yB8mhAs8zu_yd5zetVM-MhrhojBcRdXuxZra0415TUcxoDT8ZGi4qtBep-w7iKHhwCI3B_iYXURMOsbO0erKRO3jWM3lNtLdv0XQi4Pk82Zn8U5KrtDVR9MZ4IJQUOrBMVC_sA6p1EQvX6se9TksPF6d46sCKj3BXKFcqytRAvLzET6HObdR3wosE9qf77Haff02ZO9lOdUl0RSyFH6Zo1wkrydhFkcq9zYKS-vVcybX7Lve-s7a5prl_e1AKSypE0YjSy2vmxfgdew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview > <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: 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! > > _______________________________________________ > Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1Yz7qhO4Y6GvGX-UMc3TpFZmJ0IU5DRgQFerJiHP4PEreQwOm9skP5b4aCj3xJe56YoHJNN7yo8vkva5prXhQu0N_hsOijU2sKG8ribZHex7A4L_5d5CHFkgvmoYhN2w32RFwCRz1-3GO7GEWZuPT8xCSZZ32znLb4Z-fmtWDdgJQ1hgpS8yYVXU1sXNzhguZ83_QKgKrLuaPUex106KLyQsfF2_7umrwqAVgMC3BlLrhYA2xcfWSvQOhg7KajR6z_L6_x_YJhsik3HtXoOatra57bPpG4J_P-VA9YCl7ZJmkrysXw3_YMv9FZJHa5p1Kye1JS9-ou33SHESGm09_bQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1tjk-1pEga_TJu-uUdpweAeqPVVd_ormQmYpZEYGGVTSlOfuLiTatwouAM1urrF2igv3LP4WcYL7TwEht1jfyeTc9H14FVW7oZH4JZKva_NLTlccQ_YRLdlA8gp9wXfmlGprIED0_Uc7nl0rWM-zpZ6VAyJZ72DfDY05abK1A038AknnPl4Xj9nDY5qpaMG4NV-hKcE-JBnrVLvb4y1hbCrA0IZpcsHfpw2W7QaaFr88tOOrTGLKfMgoFRo9d89unyVO53zTz3MhK3XwOO6UbKQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1Yz7qhO4Y6GvGX-UMc3TpFZmJ0IU5DRgQFerJiHP4PEreQwOm9skP5b4aCj3xJe56YoHJNN7yo8vkva5prXhQu0N_hsOijU2sKG8ribZHex7A4L_5d5CHFkgvmoYhN2w32RFwCRz1-3GO7GEWZuPT8xCSZZ32znLb4Z-fmtWDdgJQ1hgpS8yYVXU1sXNzhguZ83_QKgKrLuaPUex106KLyQsfF2_7umrwqAVgMC3BlLrhYA2xcfWSvQOhg7KajR6z_L6_x_YJhsik3HtXoOatra57bPpG4J_P-VA9YCl7ZJmkrysXw3_YMv9FZJHa5p1Kye1JS9-ou33SHESGm09_bQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. 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