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Hi everyone,

I’m running a brain surface ROI analysis using data from the HCP. I need to draw those ROIs to be in annot files format so I can use them for further analysis to calculate sulcal depth (https://secure-web.cisco.com/1BjH9by7q1Ifs37LZrnji4YAMniNy1LLAc_r-1HVnNxAivi... https://secure-web.cisco.com/1BjH9by7q1Ifs37LZrnji4YAMniNy1LLAc_r-1HVnNxAiviOS6j7BLI1bWCGJITkMkYVGGvQOAIQodS4VHpSHDkldDyXZKG4rKNlbhxaqpngwqoan5SVwNyMM0Szzo8j25dUMaVWO8Zi_0h4Ub6tOO8jwDbdLO7o96JmhBLYRFdo1w89_zTkyyU-TBSgZgAEy3ji_IzKDSH1LVeS-uNtmVgD_I0kD66sF7ftfeEkkO6pWt-NE_jGzZtHOc3H5T0dJ2wi4_OfSBwyDff1ylYqjbIKEy4SWiQtfyzhtbXih6-ZzS8WX6z2i4h5pxXDSNiSx/https%3A%2F%2Fbraininformatics.springeropen.com%2Farticles%2F10.1186%2Fs40708-019-0098-1).

I draw all my sample (n=40), and to proceed to the next step, I need to measure the LGI in each subject. In some samples, I faced a similar error to the one mentioned in this thread: https://secure-web.cisco.com/13Nu69ZC35kQC9epIBWd44yarBEBej9ZnSy-C1Z9Zpg_srk... https://secure-web.cisco.com/13Nu69ZC35kQC9epIBWd44yarBEBej9ZnSy-C1Z9Zpg_srkeyznyNRcMcRsM0CPLnKEYeqUXatjHlbHL--R0zAImneDThcBOtH5DZE11NsTDai4iaBdga_qFAcVBQvz45NF-YTq1s61wrCNDvNrPLX1M2V8Yx2Z4H-r6e-bdXt4iWnx-3bdalCOwQO-RIGVPSCc6Vc2LcR5RLGgDam6ge0DVTGR-F-argW-KkUibkvWBtDb95oll9slDONBldBRbcarTfwOVkvJeA4g0cUfxIIcgD4mrH2Gjmx-M3JV4eLU41TKdZ1Wgk3yyry7DXW72g/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09799.html I tried to run the recon-all lgi again the error remained the same. I did as recommended to run the recon-all -s sub -hemi ?h -autorecon2 & 3 The new surfaces were there, and the recon-all lgi worked fine. However, my annot files were not OK with new surfaces, and I don’t know what is exactly the problem, but I will attach an image showing how the labels looked in the original HCP data brain surface and how they look after the recon-all -s sub -hemi ?h -autorecon2 & 3. I re-downloaded the original surfaces from the HCP database, and it returned to its normal display. I hope someone can help me to solve the problem, and I appreciate it.

Mudathir