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 <ronahann...@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 <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/1Y8S9-a_aN_4cgLVYzzMDZwmVbOKBrAKdYBb-6gjhmIB3m2z_nJrGD0k3Dqm9kUIdqgsoqoI4_LAlH3njosvjU6RBmCTFlLmb22bEHY78UQY05LT86x4ztIg1sBJKa0fm3goLOLR4XGkyD9Aif7yl2R5pvD0KvIzT8xeHot2NSbAadPimjX0p68AbDHBwe63QpAABsAnQRmxJix0lK2EYvQ2MgrworvfUP3wvu2Yx4exGKwXp0ICkBm6AizPEe8l2Cy0xjqywFmJZm3WKpsF2fL0NaXAh0qxwvwhkQcvbW3n0lDwWmPmnNdz904GZ883wT4NuQJN6vYCIe0iCWEZipg/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/1yrCkhsuCZJttGw9JxlZyMxFtwGGpPfILOaI3FApMIr0_5i_SEcF-a0gjI3y5Hv1IXg158x6LFbqNnK-HXGPK-Zo-skju7BFyjxVY7lsewkXklgA9fMH4PQfK4lsnV9s-hmoB25Z_sLjcdHakyMUZRQu3U6CPwnYhf1HeG4zgZOBvNV47VNh4no4sh8Pks8lX4bHfl4kfyQbJgQGLn8ORU1KvWGBRnCA6blBH0gY7A0Shnk7ZeIaxTQ918WThjpkGp5qXeF9kbiIM0rr7G2RpmCSXyr-6Sj_MVTPjuS5rTfaKkza9pAfyxsOZOIf1HWEb0cmByFvKsUh25RHMM_lFfg/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/1yrCkhsuCZJttGw9JxlZyMxFtwGGpPfILOaI3FApMIr0_5i_SEcF-a0gjI3y5Hv1IXg158x6LFbqNnK-HXGPK-Zo-skju7BFyjxVY7lsewkXklgA9fMH4PQfK4lsnV9s-hmoB25Z_sLjcdHakyMUZRQu3U6CPwnYhf1HeG4zgZOBvNV47VNh4no4sh8Pks8lX4bHfl4kfyQbJgQGLn8ORU1KvWGBRnCA6blBH0gY7A0Shnk7ZeIaxTQ918WThjpkGp5qXeF9kbiIM0rr7G2RpmCSXyr-6Sj_MVTPjuS5rTfaKkza9pAfyxsOZOIf1HWEb0cmByFvKsUh25RHMM_lFfg/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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