External Email - Use Caution 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/1k1b1WDzayyyD0xHY4p5-vf5EdJF_BVSuSDFQcDRugrS488ehdTeSW-0-0Jlapa98Ol5ZJ9N2omu6Bxq8qt5cYlJODgmoi845cOZDQP0D_ARPiMUYRTRLJ2W6BPuXHqlcL0D07An8slriOSp7kS8YvvJC5kWY_JBoNRUzjYIaZtBjjjZvDf-DYuRvm5bPE8MSI4Dvqbyp3mWwH-Y-C1j5xSqd_3vNPutIz6CaRAGywYjZKNiky50Oo9yBEQT1B16qkKZeLiIqvjgwT9lg0I3oIzipmUTDQHoYZYW-c8ak8ykSmTHCsrCiwIMdlf571zqWHFDIS-7M-Mj_mJaMj6JYQ7hdpFbg4d7LfTX_hlTq9HE/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/1_8XmxvRbZSBp8vlssv5f96XGhOV-kD7TmcMOZu9ceM-wByLK-dGi8xge2C82RA2k86hg-wQDsIH8XlTvO5fXioB9lg2FfEv5BICB0WWt9OgK6aiU_q5BnngSnXCr3VJX0fF7vZ4IgwrADIMg2hY0irTSS8jIjunBPD86amunMKz1zl1YsF036G-GdYX_szrpyfDqpJrPMKWSatGKjdbAnolEdkK0Nc0rs0zrVOWigO7IiGc2MsOytXxJU0EgfRd5qvdse0lhsNzWSyQhzpuNfZo1nsAMAfJqAklpjjxlJ45nu3Aw5P2lPT_dKT4trAtOowizAOCs8onC2P3P2KlyLARhcwq2OAQjVeLtH9ua0dU/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/1iVWlMwhruJ8V8BtcPHlMoGQOqnx_2baRSerN2nmctlGi0aN1n6XyByCkFpCbxkzAVFJcjFLEw9S8ur0mcGPKC6mgsf3XgZuL9mDt6nl5e9AeMic7VSloD4-4C9BLul-CWgZCcoJPg5Wgfai_0aZLB7fdx3wQPjlU_I9pFpphtPU-Zdn1fLlipwu209QETLuvyfM9bOKFL2l7Il8GxJ7z7YTXP_lNoxODJp1rQNAKjIJ7BIVFlLQUgBeLsbWsGGzZbFDApDBXcYWTALB-qePoWpDN_Hmfv5WCxhhl0XyoccXZIDaY3ffS0fwz_Mn51VtlHQQenuB01TnXplZnuSjlpl7oGS5CgTBgIHncFrKr7oY/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/15-8S7r3lU0XDOIlrdxpOnDhx0fy3ryeu6Aqb_HnL7Ku7kLYxrk2vMN2WFQm9Rat8MkZr_jIc4MFw6tLPOiBy9FozcSwChVsqvwnJ8BL4ElBOGP1t9VfdjZkOV00dsW7ZQIoF2Pxv2NehIrYR0fuiUoFyVeJyzCPp2LJ0ncaN4Ib4cN3TU-2Yv0Lq1Hkx25lJ5L2PdMPBhijgJxRlU1u53IF0dgaFSzUJAvADnGtnfSWCRAOdKQHyn9yJwqCaVvnlaDEatp4X_xpHOAqor42tyAu-JBiAnnDpGH2w9tyfV_jiGf-RrQ-0rprnqICVFR_VDgWJ631OpA4KwmOnAhx6oNSONd5fzFphN1DKXdNln24/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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