External Email - Use Caution Hi back,
Should be alright now. Please try this link: https://secure-web.cisco.com/1LYPTJn0s7YjdWTtPFS55k3z-IqjPfKIscsxsCg4qgjYm5i7hgZ47NYZ8BRHgQAtw4DZhP0bO52JhFFLI8LcEH2uXcDPnyyn6mXbi2PEZLkzub2KbFSDNMpQcj-DHyeMAdbjU8od-fcAnsd58VKB5nnYprNNUzbu4SeyZphucXtmwJOZO8ypI5PpTsAfrzXhwXhBNxFn7nI-I74hjqFmpZsF8mA4qlZouKMphk5t0qqcAKNcUjlISrWw3lxT_thARtkXppnJtpXaAU_6HUa3jcMs4Rjb4q7eJYv4jInujKXvt-OTVCGaGH7L5CAzEi3vhLtLwE1xKy4Hn046eARCCbdUuFPK4RiHKeapu1gceaxc/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1pkss2G7AYmlrCWYPVItnctl4W7H_OV7W%3Fusp%3Dsharing Thank you, Ela Yendiki, Anastasia<https://secure-web.cisco.com/1wf8C3YO1WyS-YWBqd1FIfHiVK5WKqJYR9c8ieJsomTQrO0f2-rZhZYTt19A7yMjjFyuEwnVEKgv-CFW9AaEmt0U8xNsK6PWpIcfueGx_buYM3Y7uLe8M8QKRmRmJ01GP-w8pVGwIf3INVl23eUTqNQuM3cfS_-hTqXe-F2DujJJx2jLBn48GzIX8g1VcNwXWCQkxYd3UppOJFSp1wFxZxWQSDSMpv7fhFcoVBE-lI6v1JuLm-_P6C0o_7cGAFdLqsmpR157fvT6Y2uCrFY_hCsk_EgLHFPaD4KWzMNFZbayU8FoPgIloLLv7GRPzueQKaPZkLZzgk9quPbHRgoC45gHCwGwNdxiVpd29CX1WarM/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Yendiki%252C%2BAnastasia%2522> Thu, 30 Jun 2022 14:18:47 -0700<https://secure-web.cisco.com/1R24_YWa3I-ukmPCtAps1i7B2qFjI5U2gpseCL8fDHwzXaevHkEVG7trWV4Cj-gMsagngoIB9mEgkrPC1RklIfCR4SE31EKOud8FSq8d-kPZgPLTTQmhXyg64yN4MIeVnR0HBdIDhD8NPfVoQwjb3mLXF7iA55jUY0U3eXQ8hzcYRstmt8gABDevgMqGwaJ9jdqLsMWhUWCrA0lH95roRl8E_ITaAr_I2jYAjE6qmovtyV6tw-xN8zT5za9fDhbsdEFhr7R2KEHHia5d1UpRKdMxb_Tiy3HiK0TnRM79ZwVce_r9gyo_8La33TuqSuRvQKRHIMuY_SwF_Jzl0U5wxjMTcgPlzgMM21l_To59yyS0/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220630> Hi Ela - Can you make the google doc accessible by all? Anastasia. ________________________________ From: Salar Dini, Elaheh <elaheh.salard...@yale.edu> Sent: Thursday, June 30, 2022 5:08 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: trac-all -prep -c ERROR Thank you for the reply. For some reason, when I change the DCM file to nii and look at them, in majority of our subjects, the cerebellum and lower brain stem has been cut off, but in this specific subject, I don't think the CST is truncated or out of field more than any other subjects that the TRACULA steps have been run for without any errors. I have taken a few screenshots of both this subject and another one whom -prep and -bedp have been run for without any errors and uploaded them to google drive. Please find the link here: https://secure-web.cisco.com/1LCiPLQmcEsS4BCM0TJyZvxoi4nUKpJbfm_yczRtTlOqrMH5KpC7za-O8r7lqyFo-JyQKsclGI6CsTUjZrwJxa3LFt8Ra9TOXhcNICwqqPUCIpCtvGPg4fqvlheBZR2BgjDNUu8hlXxa4ooX5LTkyJbVhKipqSUoeaZPNuBfy-Tn3KOkwcImJ-NHThk6DVLD96Kfh3PNkMKqp0qWVYGY3P2kYyJuMFFaUTeEYSD0-suXOIWeDjnKSJoF62YOsqErHNxdilp773bgtuS8lcggEjYnlLrvL6n4AMteFS6Pk3cAfRKTD-Umy8DmTu6nUnKenIJ45sDXFiWIZ858fNzUiEgIgVme2ETnqMINE1Ee7WsA/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF%2Fview%3Fusp%3Dsharing Moreover, it is worth mentioning that this specific subject had profound global atrophy with diagnosis of Alzheimer's. As always, I appreciate your time and help. Kind regards, Ela Yendiki, Anastasia<https://secure-web.cisco.com/1wf8C3YO1WyS-YWBqd1FIfHiVK5WKqJYR9c8ieJsomTQrO0f2-rZhZYTt19A7yMjjFyuEwnVEKgv-CFW9AaEmt0U8xNsK6PWpIcfueGx_buYM3Y7uLe8M8QKRmRmJ01GP-w8pVGwIf3INVl23eUTqNQuM3cfS_-hTqXe-F2DujJJx2jLBn48GzIX8g1VcNwXWCQkxYd3UppOJFSp1wFxZxWQSDSMpv7fhFcoVBE-lI6v1JuLm-_P6C0o_7cGAFdLqsmpR157fvT6Y2uCrFY_hCsk_EgLHFPaD4KWzMNFZbayU8FoPgIloLLv7GRPzueQKaPZkLZzgk9quPbHRgoC45gHCwGwNdxiVpd29CX1WarM/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522Yendiki%252C%2BAnastasia%2522> Wed, 29 Jun 2022 08:41:26 -0700<https://secure-web.cisco.com/1Rwf6Ju98IUds1-ksQMMvkZ8Vyh2LRDaANaR0F8ksDqkm2-z_pd10ugD7j6bGvQo1WKxqUunFKfP8FBZQ8RWOYFrSPRzzlxPoT7G29AEmdMT-KFc2mjoxRQbiCJ0ykyNBN2V3AMh68yAADJA6A88q_7XHsRH_FAa2gKhs1oJz2d3MCjH-azF1Y1PEhwWRBMkRrNwgGdVq9PJX1M873iqClhRuprGr431uXj-UGZfXqjrGmGKP7niFxXw6EoiHhTOQDyIlvMMeh68yF_0WAkvJPf8VS3Fc134UOZUOg6XDygkI34cDB0UG9tt5l5jpYqXanXPZ1ACE4QI6lvPJdf1mhytQHUxlHqXIMpr2CTLdM8U/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20220629> Any chance that part of the left CST is truncated in this one subject? E.g., if the top part of the brain was outside the field of view? Anastasia. ___________ ________________________________ From: Salar Dini, Elaheh <elaheh.salard...@yale.edu> Sent: Wednesday, June 29, 2022 11:38 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: trac-all -prep -c ERROR Dear experts, I am running TRACULA for 90 subjects. Exceptionally, for one of the subjects, I get the following error in -prep step: ((INFO: Distances between consecutive points in test subject's space are 10 13 12 13 13 12 WARN: Could not find satisfactory control point fit - try 17034 Writing output files to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_* Writing spline volume to /home2/am2359/fs6_data/TRACULA/subjects_dir/47/dlabel/syn/lh.cst_avg16_syn_bbr_cpts_7.nii.gz Segmentation fault (core dumped) Linux tauruspet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Jun 29 10:31:11 EDT 2022)) I am attaching the log file as well: https://secure-web.cisco.com/1VB2DQSee7yLJ8655gJ9lHS6jTYDjez-TCvT_cO3K7WSf7tA1x0aK6xNqUXDFs-AJt6WJEL1MECXC11d60wSApHUKdkLFNvmMfEbPuPUUAtFs_4fKyFpp21hgKrrD7icJ10wyjjQXb8vg4kNiFcg0ZWK6d-nBO900fz4qtBX-RqHfe5VTrWMPV0HaxbgW-CY4FyjUfC7wiJKM0blP0-Rc-M084jdAfnkhfZgwre4f0RqIMDQhc9vTA062B62V7YihRWnkliZ_4qTqmI3U1ya99xxN3v65fmXKWOeHeaQPnrfMLFHZAdQlAWEjJNW6l2wP_LD6jqOK8eY9Jj9stzYnqaPwa0Z95vQSoWlY5UvxzHY/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy%2Fview%3Fusp%3Dsharing On a quick look, aparc+aseg seems to be properly done. Will you please help me to troubleshoot this if possible? Thank you, Ela
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