External Email - Use Caution Dear zlseu, We currently do not have an “official” release of the probabilistic atlas in a reference space. It is try that some of the smallest nuclei may not appear in the hard (discrete) segmentation, but you can always use the option to write down the posteriors. Then you can open the file corresponding to eg the Pt and see the soft probability map. The instructions can be found in the FAQ section of the wiki: https://secure-web.cisco.com/1WLdU6eWp0r0oi5ZtLH-suvhQZo4bilAef24xA5DF8-Fi-v5AuWY0kev4cPDXtc9E_VsbMINXUilb0MyrjeY75RhchrN-K1fikBcUwTlzb3ibesKeUfKa5XIOQk2o7cNFAO4rS_psUvK_0UgNj9dufW3xKF2i0cDeMqShZslclPyM0zEZ0trdbOA806dWBJSCUjQogBA_YFuS2sEMq_pLvPVnc3b7aRrTb1SHTdMTkAopeVzEvsZkaRFe_SUK10Q3gRAC3-95-wSvGxs6_wclAA/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2FThalamicNuclei Cheers, /E
-- Juan Eugenio Iglesias http://secure-web.cisco.com/1mOqS3QIf3uAWOF8-fWWdyr8xCbchx5YP3crK_PrmzkU8bQbWkR2Sj6CSMSIj4CgLoTofHc595uu6q6XcwfzYvLER-9qrxo2lS3RXnbvn2yYujjew7sy8bXptnf1BRvEXOSPpoDWGyKToEC9_1yy5kdyfUMK8btlLGeuV64Z6gRhrmwulGPgPfRmSwHExCmfO9IHWPes2bYOmJ_rm2c-1vdnxDZvNZGb_FNN8r5aU8yLIw4zWInwxaHEQ39UCHlUtGMr2xW6RkR2vCEotBai54w/http%3A%2F%2Fwww.jeiglesias.com From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of zlseu2109 <zlseu2...@163.com> Date: Monday, July 10, 2023 at 9:11 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Cc: chm...@163.com <chm...@163.com> Subject: [Freesurfer] some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz External Email - Use Caution TO: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> FROM: zlseu2...@163.com<mailto:zlseu2...@163.com> SUBJECT: segmentation of thalamic nuclei error: some thalamic subregions are not shown in image of ThalamicNuclei.v13.T1.mgz Hello FreeSurfer Developers, I’ve segmented thalamic nuclei via thalamic nuclei atlas and gained volume result of 25 subregions of each thalamus, but some subregions (eg. Right Pt) cannot be shown by load ThalamicNuclei.v13.T1.mgz in freeview. I'm attempting to use this thalamic nuclei atlas for functional ROIs analysis, using other softwares (eg.SPM). Could you provide .nii file of this atlas? Or can you help me show this missed thalamic subregions? Or how can I transform the file of thalamic nuclei atlas in FreeSurfer pipeline to .nii file. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-ubuntu20_x86_64-7.3.2 2) Platform: Ubuntu Release 20.04.6 (focal) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be <https://secure-web.cisco.com/10UJioIagz0Wb9TxkEGENkRKFPUs6Hmk98CJpO8LTMIGPBGrbOeES4rKHrSHo1bmDt5d7nzGawhcGrXRRrvcBPchog43DBoAjbx5YmZCmQHzM0eU64B1dbaVgPR2V3XNdKXsM5cOFv0d0K_xAMqWL5rOt_ZN2S3rUQ3GdMIFHioYWf7cO_euq6moGl2HTFtx7dgTmRnmyNq5sgRRJ45W3ldMrnRXCMkdzQXR9d1r-99HSBNjnOLEDUdwgym1M7WZ1kKe3mvdFzn9iY5xXmdGMPh40mUZ5LO9DfQqafjTH1XMAXuRwP5u6ezTAEbr9gDz-EGzd0NvRC97EcoZThI8b_g/https%3A%2F%2Fmaas.mail.163.com%2Fdashi-web-extend%2Fhtml%2FproSignature.html%3FftlId%3D1%26name%3Dzlseu2109%26uid%3Dzlseu2109%2540163.com%26iconUrl%3Dhttps%253A%252F%252Fmail-online.nosdn.127.net%252Fqiyelogo%252FdefaultAvatar.png%26items%3D%255B%2522zlseu2109%2540163.com%2522%255D> [Image removed by sender.] zlseu2109 zlseu2...@163.com
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
