External Email - Use Caution
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/1SmnY7WYnV1XRZV1hzFK0-fljtz5hTgSEDuVurOZOZqB22z... On a quick look, aparc+aseg seems to be properly done. Will you please help me to troubleshoot this if possible?
Thank you, Ela
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Wednesday, June 29, 2022 11:38 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all -prep -c ERROR
External Email - Use Caution
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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy/view?usp=s...https://secure-web.cisco.com/1SmnY7WYnV1XRZV1hzFK0-fljtz5hTgSEDuVurOZOZqB22zXjeNXjwoJmMg8m0rebhhkBgEG85lX60uQdweaszlFaJK0aAf6k-tDqRHPeCrz3HbLV22IVyX0RGrImMTcUBc_63gMzWjWK9eyH69Bjr8g1UyxZXFkNJ3OsWaVuwX97x0BWhtcbbrQ_LY-JCZgpxP_XA6lSuz7dbq1KXKfR7hYJkRBpmu-dwHdY2yz8QubiCBLB8q20-RD8dv0uLOM-aXyamfQOU9KFfOAuT1t9aehuseGannHIdY4Fq30y2JAnFZ42owKAg-cUAjR6_wDxWve_BGI77yzfLgDi7CusPY_0vml2btWwy8N3p1xjaHs/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
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_BVSuSDFQcDRugrS488...
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, Anastasiahttps://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 -0700https://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.salardini@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_HnL7Ku7kL... On a quick look, aparc+aseg seems to be properly done. Will you please help me to troubleshoot this if possible?
Thank you, Ela
Hi Ela - Can you make the google doc accessible by all?
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Thursday, June 30, 2022 5:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep -c ERROR
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:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF/view?usp=s...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, Anastasiahttps://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 -0700https://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.salardini@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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy/view?usp=s...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
External Email - Use Caution
Hi back,
Should be alright now. Please try this link: https://secure-web.cisco.com/1LYPTJn0s7YjdWTtPFS55k3z-IqjPfKIscsxsCg4qgjYm5i...
Thank you, Ela
Yendiki, Anastasiahttps://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 -0700https://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.salardini@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_yczRtTlOqrMH...
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, Anastasiahttps://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 -0700https://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.salardini@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_cO3K7WSf7t... On a quick look, aparc+aseg seems to be properly done. Will you please help me to troubleshoot this if possible?
Thank you, Ela
Is the brainstem cut off from the diffusion scan? A bit hard to tell from the pics but this could be the problem. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Thursday, June 30, 2022 7:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all -prep -c ERROR
External Email - Use Caution
Hi back,
Should be alright now. Please try this link: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/drive/folders/1pkss2G7AYmlrCWYPVItnctl4W7H_OV7W?usp...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, Anastasiahttps://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 -0700https://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.salardini@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:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF/view?usp=s...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, Anastasiahttps://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 -0700https://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.salardini@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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://drive.google.com/file/d/1pgEmkMtk4UoELpGR2bU_Vac-2BDr-eNy/view?usp=s...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
freesurfer@nmr.mgh.harvard.edu
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Salar Dini, Elaheh -
Yendiki, Anastasia