Re: [Freesurfer] memory allocation error
External Email - Use Caution dear all, is there any progress on this issue? can I send more information to help with debugging? judging from the other entries of the mailing list this is not an issue that concerns only me. thank you for your attention, bests fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1dOZP5j8XdDioY7tViTW7NqEi9mrvvba6PAbK6uv63gP7Q8bNrlLCYFkKfvXXNpcvR7MIg3L5wRfoQWO66UdM1HtJA4W7iKqfq4FhnnE9W2R2KwGDIaI7MjIpsOL5VryAdycFZZismV1CFp4rNE47COVEcaN7m-ypDnjnXobdlMmq5EirIKZSBuBmmU3BrEdMYwD-BFb3nS8AdCafRfCfvjcSJaTNtkXlb52Ab49xmqiAfSbLVpAV32A2F_b5QaItKY0wLlYGCGD0ZC1nbr_gag/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1C5zQD6S2aQEn7dMGBOKijRrWY8INlUWuanF5g6gCvX_Y1b1F-tAXUd55vvYP2ExpFYOE4G_Gf0Ujo0hS1Y2GnTUxWS4Q-Hw7ryBf9XfzTCb8akQhMElGzETBV9Y9Dx77zF8x-MJ9GUD0FyloeWVletfQc1s8UEKQ3yoaKTFfJ2V8wWshKFJa_JP1qacQoSHNmMiXI_FcftEAwml4E2oNwVLDD4wbGRONmoBUwVEiXo5dl7kMXPeg0RsJWGcPzoL3tA375bU9hNlgebAeMlJOhg/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1R3-Q2awQvkHA7pJ5-Bypzc-0X_unyiumlI9PjumZoPxQt07p2OV6Ic1U3XRYL4eNBJal5v0TRUTOvxYTlIeLC1WTMxI-rtEtG8N77JaaMIF13TDkl5R43K7OsP1ahBNt1eNtB_F2H91UBJElxnZ9OxetTmgwCn-WoMBTZsXBsH7BO7zP_6eZ54cIYpYTvBuEgv1DwLFBLnNlUpt_JuYJSDx4zM-kLZt3qrNjw67fNp5cbpAoaJCV0cCgR2NfJCsLdepyT15Wfal__W5aiZ2SPg/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1R3-Q2awQvkHA7pJ5-Bypzc-0X_unyiumlI9PjumZoPxQt07p2OV6Ic1U3XRYL4eNBJal5v0TRUTOvxYTlIeLC1WTMxI-rtEtG8N77JaaMIF13TDkl5R43K7OsP1ahBNt1eNtB_F2H91UBJElxnZ9OxetTmgwCn-WoMBTZsXBsH7BO7zP_6eZ54cIYpYTvBuEgv1DwLFBLnNlUpt_JuYJSDx4zM-kLZt3qrNjw67fNp5cbpAoaJCV0cCgR2NfJCsLdepyT15Wfal__W5aiZ2SPg/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Gesendet: Donnerstag, 20. Mai 2021 11:17:05 An: Freesurfer support list Betreff: Re: [Freesurfer] memory allocation error External Email - Use Caution dear Andrew, I was allowing 8, 16, ~36GB of memory in different runs, so I would exclude that this was the problem. bests fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/187My4Jucq7g2iOhroEKk8K8OFGoFoeORTu-mXzokMtuySZfRpdmpBUHAWrZs3PiUgTJQxvI4t7mF19Q65QoVRPm9HIRo1ga6iFYC3emunkTnsx44xyypE8RQ7se9eW1WnrqXrI_Z3OCRQDKjl_O6YrVXw8u2fxs-M2rmDvVwA1c8A6B-TCU2kRIeB7oIt49DW_DM1zE6Vs2u2KvWqA9-ZtIcGYVGPwCKGzShIT5OOvNrJjUldtN0AoNqCDk2gUFd6DjRtozUhmyNbDtaEpIJOQ/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15nLSigNtaEzdHxIpWerC4ukwoFMkkmjnCaSZHFWvxZoHCXH4XhBy49dgkjt_Vq9EFKvYq9xxQ4wmBIAl28GFHwhUJe7IfUAQkVKEMD5fvpyeYO8Shfw1PZr2zy9p7hm86gBaVav8UarY5wXbQ2FUH7lzmO3kgv-sylrFq8rFfmbsx-WSHLLJyi6zQDOV0A7vxj7uJyZDym-vCiDaPrxTdvo7Tws6y8FnBWgAvc-2BMa-GAAkHZJOPrvFuJw9Nh5WXnTa0wo5mD-Qgvp8aHL22A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Hoopes, Andrew Gesendet: Mittwoch, 19. Mai 2021 20:38:45 An: Freesurfer supp
Re: [Freesurfer] memory allocation error
External Email - Use Caution dear Andrew, I was allowing 8, 16, ~36GB of memory in different runs, so I would exclude that this was the problem. bests fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/187My4Jucq7g2iOhroEKk8K8OFGoFoeORTu-mXzokMtuySZfRpdmpBUHAWrZs3PiUgTJQxvI4t7mF19Q65QoVRPm9HIRo1ga6iFYC3emunkTnsx44xyypE8RQ7se9eW1WnrqXrI_Z3OCRQDKjl_O6YrVXw8u2fxs-M2rmDvVwA1c8A6B-TCU2kRIeB7oIt49DW_DM1zE6Vs2u2KvWqA9-ZtIcGYVGPwCKGzShIT5OOvNrJjUldtN0AoNqCDk2gUFd6DjRtozUhmyNbDtaEpIJOQ/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15nLSigNtaEzdHxIpWerC4ukwoFMkkmjnCaSZHFWvxZoHCXH4XhBy49dgkjt_Vq9EFKvYq9xxQ4wmBIAl28GFHwhUJe7IfUAQkVKEMD5fvpyeYO8Shfw1PZr2zy9p7hm86gBaVav8UarY5wXbQ2FUH7lzmO3kgv-sylrFq8rFfmbsx-WSHLLJyi6zQDOV0A7vxj7uJyZDym-vCiDaPrxTdvo7Tws6y8FnBWgAvc-2BMa-GAAkHZJOPrvFuJw9Nh5WXnTa0wo5mD-Qgvp8aHL22A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Hoopes, Andrew Gesendet: Mittwoch, 19. Mai 2021 20:38:45 An: Freesurfer support list Betreff: Re: [Freesurfer] memory allocation error Hi Fabio, How much memory are you allowing for this process? You might want to just try increasing the limit on the slurm job to see if that works. Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bernardoni, Fabio Date: Tuesday, May 11, 2021 at 4:22 AM To: freesurfer mailing list Subject: Re: [Freesurfer] memory allocation error External Email - Use Caution Sorry I forgot the attachment. Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: Bernardon
Re: [Freesurfer] memory allocation error
Hi Fabio, How much memory are you allowing for this process? You might want to just try increasing the limit on the slurm job to see if that works. Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bernardoni, Fabio Date: Tuesday, May 11, 2021 at 4:22 AM To: freesurfer mailing list Subject: Re: [Freesurfer] memory allocation error External Email - Use Caution Sorry I forgot the attachment. Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: Bernardoni, Fabio Gesendet: Dienstag, 11. Mai 2021 10:20:19 An: freesurfer mailing list Betreff: AW: memory allocation error Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached): https://secure-web.cisco.com/1my6XFSQF3uEj1ZrgriH6ZF1WxWnqfBMBdiuPDNdXZfq_XO9uhiKwZPYEvG3NS0vJSxZM7hcmTWq1hUXJUt2_XigG_UONfGk8UL_5FWLEktb3qrFvDpcgohhnKOb1j6uAWMIE10PVwXrnLZx4Gf441Olp7jcMNX8eLVVNtPMcFPE5OH3N4cODD6Z83hDSq2HPzZH7tQ78HFekvVecIFyNfG7sKdlEVUVjwFGX6pd4c9fRkVgt6eCj-kuSxbdQrF2OBr2Vi1IX-Bz_UzXD9ZcLyw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html my FS version is: recon-all -version freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e and I did not perform any editing, so there is no control points to remove as suggested in the above post (which also refers to version 6). Therefore, if I understand correctly, my problem is a different one. Any clue what I might be doing wrong? Other possibly useful information: uname -a Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux Thanks for any hint/help Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbN
Re: [Freesurfer] memory allocation error
External Email - Use Caution Sorry I forgot the attachment. Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 Von: Bernardoni, Fabio Gesendet: Dienstag, 11. Mai 2021 10:20:19 An: freesurfer mailing list Betreff: AW: memory allocation error Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached): https://secure-web.cisco.com/1my6XFSQF3uEj1ZrgriH6ZF1WxWnqfBMBdiuPDNdXZfq_XO9uhiKwZPYEvG3NS0vJSxZM7hcmTWq1hUXJUt2_XigG_UONfGk8UL_5FWLEktb3qrFvDpcgohhnKOb1j6uAWMIE10PVwXrnLZx4Gf441Olp7jcMNX8eLVVNtPMcFPE5OH3N4cODD6Z83hDSq2HPzZH7tQ78HFekvVecIFyNfG7sKdlEVUVjwFGX6pd4c9fRkVgt6eCj-kuSxbdQrF2OBr2Vi1IX-Bz_UzXD9ZcLyw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html my FS version is: recon-all -version freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e and I did not perform any editing, so there is no control points to remove as suggested in the above post (which also refers to version 6). Therefore, if I understand correctly, my problem is a different one. Any clue what I might be doing wrong? Other possibly useful information: uname -a Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux Thanks for any hint/help Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
Re: [Freesurfer] memory allocation error
External Email - Use Caution Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached): https://secure-web.cisco.com/1Ip5HtCg9MqyghYHl20NFxCMImoJoShIH1y6ytQEK2tKtD13Oz0AIBueggTl_ahZFc6uNPUz7V5A3mUmh5acqtEUgyjJdjPb5JMcglhVsNmdkpAzFguuG2x10cblbsfNFAee3bxX5k-azvnAx_hKV1PE37o4wXcPwHktYZyVK41CFA6ORc_6kYF6Oeggr2XYVTNetiT3e1BLbi48zEiKnO6voUBrNf0s8ORynZS2fDVBP8_N97yBlOqXg0rHCaZ7J/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html my FS version is: recon-all -version freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e and I did not perform any editing, so there is no control points to remove as suggested in the above post (which also refers to version 6). Therefore, if I understand correctly, my problem is a different one. Any clue what I might be doing wrong? Other possibly useful information: uname -a Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux Thanks for any hint/help Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/15HwLpU5VlSqNSJlIROcqXzy17m5cEVlxA22c1BhqN_Pd35FjWpytolF845HPS01awNT_zQjyBI2m111j6rfITVzmgLONDhN9TsY6iqtWtRw-L7GGq_-D5Xe21auR1Uzm7UWoNQc2NGcHCtRsew025Yy1KQK2P5a5dJswZWaaed3oc2q387r4yCuG7mURf_MvfjReKjdbI2w9pu3_3MKHhKojdohuGKOyNFXkFrpIeLdanqBd_Rb6Kp0vSlrh3OwJ/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1jdKs38Kd-Oms54JIKsH7_jGGI6wne-La9XILjLrzWQA_NwYCrBNNiPmBWfJ_PmVPghuil6_kzbBmGRYz8u9kBxrj9uZgcJLgl1dtjtS6zamTE20CMRjpQkavy0Zfopf32rVUtTXCWjk3pX34eLI4PLF2BqkUem3ZNiNDU72mvG1Of_-ecgRdUR_5gl75hvfOkGJpDLeF_nO57s-GY3QTe02_mGjrodqxZTCYnMutvYVqku1iW77jtC1zrnXzOdlb/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1MMyCALLCSmaFUzZQnggtv4g0CsExa-ayBmQqe80VwC13pQX3ciqL6MpBuoKJW4zSBsjm1-hkGi1PLKyPZE8Tcbj1pjOcrCJJkJ7qKAx5eL4RBWnLPJBAbX31xR-GlBA9FIeZDivhcuPx0hHrRUMMt4TambZSKoQKZ4iScG8Q1h4hmPSfrMq29G-B1zxH2miODaPELkxaDX1ad3onPJjTo54XUwhbPTZpw-dzwKrA4ZSl9Txu6OLhHeOAWnumjFmD/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1MMyCALLCSmaFUzZQnggtv4g0CsExa-ayBmQqe80VwC13pQX3ciqL6MpBuoKJW4zSBsjm1-hkGi1PLKyPZE8Tcbj1pjOcrCJJkJ7qKAx5eL4RBWnLPJBAbX31xR-GlBA9FIeZDivhcuPx0hHrRUMMt4TambZSKoQKZ4iScG8Q1h4hmPSfrMq29G-B1zxH2miODaPELkxaDX1ad3onPJjTo54XUwhbPTZpw-dzwKrA4ZSl9Txu6OLhHeOAWnumjFmD/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Memory
Is there any way to check how many autorecon processes I can run at the same time? I am using a linux with 16gb ram. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd)
Hi Ping - It'll make it easier for us to replicate your memory error if you send us the data set where you get the error. Can you please zip up the dmri, dmri.bedpostX, and dlabel directories for this subject and upload them for me and Zeke? https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, a.y On Wed, 27 Mar 2013, Ping-Hong Yeh wrote: Hi Zeke, That specific subject had v5.1 recon-all run by Leopard with FS v5.1 (another computer), but v5.2 trac-all run by Snow Leopard with FS v5.2 . If you scroll down the log file, you will see the /Application/freesurfer, which is the v5.2 where it crashed. Anyhow I have attached the log file of another subject run by FS 5.2, both recon-all and trac-all. Thanks. ping On Wed, Mar 27, 2013 at 4:00 PM, zkauf...@nmr.mgh.harvard.edu zkauf...@nmr.mgh.harvard.edu wrote: Ping, According to line 9 of the log file you sent to Anastasia, are running freesurfer version v5.1. Not version 5.2. -Zeke Original Message Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd) Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Zeke Kaufman zkauf...@nmr.mgh.harvard.edu -- Forwarded message -- Date: Wed, 27 Mar 2013 13:44:56 -0400 From: Ping-Hong Yeh pinghong...@gmail.com To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train Hi Anastasia, See the attached. Thank you. ping On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Can you send us your entire trac-all.log? There's some info in there about your system and the freesurfer build you're using that we'll need to try to replicate the problem. Thanks, a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1
Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train
Hi Ping - Can you send us your entire trac-all.log? There's some info in there about your system and the freesurfer build you're using that we'll need to try to replicate the problem. Thanks, a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk
Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd)
Ping, Yes, I see. We are looking into it now and will try and replicate the issue. -Zeke On 03/27/2013 05:21 PM, Ping-Hong Yeh wrote: Hi Zeke, That specific subject had v5.1 recon-all run by Leopard with FS v5.1 (another computer), but v5.2 trac-all run by Snow Leopard with FS v5.2 . If you scroll down the log file, you will see the /Application/freesurfer, which is the v5.2 where it crashed. Anyhow I have attached the log file of another subject run by FS 5.2, both recon-all and trac-all. Thanks. ping On Wed, Mar 27, 2013 at 4:00 PM, zkauf...@nmr.mgh.harvard.edu zkauf...@nmr.mgh.harvard.edu wrote: Ping, According to line 9 of the log file you sent to Anastasia, are running freesurfer version v5.1. Not version 5.2. -Zeke Original Message Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd) Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Zeke Kaufman zkauf...@nmr.mgh.harvard.edu -- Forwarded message -- Date: Wed, 27 Mar 2013 13:44:56 -0400 From: Ping-Hong Yeh pinghong...@gmail.com To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train Hi Anastasia, See the attached. Thank you. ping On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Can you send us your entire trac-all.log? There's some info in there about your system and the freesurfer build you're using that we'll need to try to replicate the problem. Thanks, a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz
[Freesurfer] memory allocation errors on Snow Leopard running dmri_train
Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz
Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train
Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train
Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
Re: [Freesurfer] Memory Consumption of GPU-assisted Freesurfer?
The environment variable 'FREESURFER_CUDA_DEVICE' defines the device number of the GPU device. Although I dont think you will see much benefit in splitting the surface processing across two gpus, as the CUDA surface code is not as optimal as the volume-based mri_ca_register code for parallel processing. Nick On Mon, 2013-02-04 at 19:31 -0500, R Edgar wrote: On Mon, Feb 4, 2013 at 6:54 PM, Zhongtian Dai d...@uchicago.edu wrote: Thanks for the speedy response. I think we will go with GTX 660 Ti with 2GB GPU RAM. We don't have a lot of subjects (as we hope to have) to analyze, so maybe we will try splitting left and right hemispheres to two graphic cards if our CPU RAM doesn't deplete. How do you designate the cuda commands to a certain GPU? You'll have to ask Nick that - I don't remember, I'm afraid. Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Memory Consumption of GPU-assisted Freesurfer?
Hi, I wonder how much graphic card memory is needed by the CUDA commands. We have two Quadro NVS 295's with 256MB memory and the CUDA commands all report out of memory errors. I know the cards are kind of outdated but I want to make sure a new card would meet the task before purchasing. A separate question is whether the current CUDA implementation supports spreading the work to multiple GPU's if they are present? Thanks. -- Zhongtian (Falcon) Dai University of Chicago ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory Consumption of GPU-assisted Freesurfer?
On Mon, Feb 4, 2013 at 5:50 PM, Zhongtian Dai d...@uchicago.edu wrote: I wonder how much graphic card memory is needed by the CUDA commands. We have two Quadro NVS 295's with 256MB memory and the CUDA commands all report out of memory errors. I know the cards are kind of outdated but I want to make sure a new card would meet the task before purchasing. I never checked exactly how much GPU RAM was consumed (having 3 GiB cards has that effect on you ;-) ), but 256^3 = 16 M. So each volume takes 16 * sizeof(T) MiB of RAM. I don't recall offhand how many volumes GCAMorphGPU had to allocate, but it was quite a few (at least 6 float volumes for sure). I can easily see 256MiB being insufficient (particularly when you remember that the CUDA context itself consumes some - small - amount of RAM on the card). A separate question is whether the current CUDA implementation supports spreading the work to multiple GPU's if they are present? No - at least not in the stuff I did. But you can run multiple recon-alls, with each using a different GPU. And with enough GPU RAM, you can probably run multiple recons on the same GPU with reasonable speedups, since there are plenty of portions of the pipeline which are still on the CPU. HTH, Richard ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory Consumption of GPU-assisted Freesurfer?
Hi Richard, Thanks for the speedy response. I think we will go with GTX 660 Ti with 2GB GPU RAM. We don't have a lot of subjects (as we hope to have) to analyze, so maybe we will try splitting left and right hemispheres to two graphic cards if our CPU RAM doesn't deplete. How do you designate the cuda commands to a certain GPU? On Mon, Feb 4, 2013 at 5:04 PM, R Edgar freesurfer@gmail.com wrote: On Mon, Feb 4, 2013 at 5:50 PM, Zhongtian Dai d...@uchicago.edu wrote: I wonder how much graphic card memory is needed by the CUDA commands. We have two Quadro NVS 295's with 256MB memory and the CUDA commands all report out of memory errors. I know the cards are kind of outdated but I want to make sure a new card would meet the task before purchasing. I never checked exactly how much GPU RAM was consumed (having 3 GiB cards has that effect on you ;-) ), but 256^3 = 16 M. So each volume takes 16 * sizeof(T) MiB of RAM. I don't recall offhand how many volumes GCAMorphGPU had to allocate, but it was quite a few (at least 6 float volumes for sure). I can easily see 256MiB being insufficient (particularly when you remember that the CUDA context itself consumes some - small - amount of RAM on the card). A separate question is whether the current CUDA implementation supports spreading the work to multiple GPU's if they are present? No - at least not in the stuff I did. But you can run multiple recon-alls, with each using a different GPU. And with enough GPU RAM, you can probably run multiple recons on the same GPU with reasonable speedups, since there are plenty of portions of the pipeline which are still on the CPU. HTH, Richard -- Zhongtian (Falcon) Dai University of Chicago ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory Consumption of GPU-assisted Freesurfer?
On Mon, Feb 4, 2013 at 6:54 PM, Zhongtian Dai d...@uchicago.edu wrote: Thanks for the speedy response. I think we will go with GTX 660 Ti with 2GB GPU RAM. We don't have a lot of subjects (as we hope to have) to analyze, so maybe we will try splitting left and right hemispheres to two graphic cards if our CPU RAM doesn't deplete. How do you designate the cuda commands to a certain GPU? You'll have to ask Nick that - I don't remember, I'm afraid. Richard ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory problem
Mia, this time it looks like there was plenty of memory, but it exited on a defect. make sure the wm.mgz looks good (doesnt have stuff outside the white matter). see the 'topological defects' section of our tutorial for info on what to look for and how to fix it. Nick Hi freesurfers, So i reran recon-all -make all overnight, and it ended with errors still. It looks like the same error (I attached the log). There was another process running while I ran the recon the first time, but I made sure that wasn't the case this time around. Is the solution running the recon in a whole new place with more space? Thanks so much, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky [ni...@nmr.mgh.harvard.edu] Sent: Wednesday, January 23, 2013 1:45 PM To: Douglas N Greve Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Memory problem Mia, also i noticed this at the top of the log: total used free Mem: 37010736 19490372 17520364 -/+ buffers/cache: 10784236 26226500 Swap: 8393952 1505288243424 it shows that just 1.7GB is available for the recon to run, which is below what we recommend. recon-all usually needs at least 2GB. after inspecting for defects like doug suggests, you could try stopping other apps that are consuming mem (or just reboot which will ensure maximal free memory) and then run recon-all -make all Nick On Wed, 2013-01-23 at 13:23 -0500, Douglas N Greve wrote: Hi Mia, try looking at the lh.orig.nofix surface. There may be a huge defect (like the entire cerebellum is attached). You can run tkmedit MG58_SurferOutput_postop orig.mgz lh.orig.nofix Note that you will get a few error messages when loading the orig.nofix surface. These can be ignored doug On 01/23/2013 12:19 PM, Borzello, Mia wrote: Hey Freesurfers, I received a Cannot allocate memory error while running a recon overnight. I think there should be enough space on the machine to store the data so I'm suspicious that it's a different memory problem. I attached the recon-all.log file. Thanks for your help! m ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory problem
Hi Mia, try looking at the lh.orig.nofix surface. There may be a huge defect (like the entire cerebellum is attached). You can run tkmedit MG58_SurferOutput_postop orig.mgz lh.orig.nofix Note that you will get a few error messages when loading the orig.nofix surface. These can be ignored doug On 01/23/2013 12:19 PM, Borzello, Mia wrote: Hey Freesurfers, I received a Cannot allocate memory error while running a recon overnight. I think there should be enough space on the machine to store the data so I'm suspicious that it's a different memory problem. I attached the recon-all.log file. Thanks for your help! m ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory problem
Mia, also i noticed this at the top of the log: total used free Mem: 37010736 19490372 17520364 -/+ buffers/cache: 10784236 26226500 Swap: 8393952 1505288243424 it shows that just 1.7GB is available for the recon to run, which is below what we recommend. recon-all usually needs at least 2GB. after inspecting for defects like doug suggests, you could try stopping other apps that are consuming mem (or just reboot which will ensure maximal free memory) and then run recon-all -make all Nick On Wed, 2013-01-23 at 13:23 -0500, Douglas N Greve wrote: Hi Mia, try looking at the lh.orig.nofix surface. There may be a huge defect (like the entire cerebellum is attached). You can run tkmedit MG58_SurferOutput_postop orig.mgz lh.orig.nofix Note that you will get a few error messages when loading the orig.nofix surface. These can be ignored doug On 01/23/2013 12:19 PM, Borzello, Mia wrote: Hey Freesurfers, I received a Cannot allocate memory error while running a recon overnight. I think there should be enough space on the machine to store the data so I'm suspicious that it's a different memory problem. I attached the recon-all.log file. Thanks for your help! m ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory corruption when performing mri_segstats
Hi Wenjing, I don't know what is happening either . Can you tar up the aparc+aseg.nii.gz and filtered_func_data.nii.gz file can send them to me on our file drop? www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html thanks doug On 08/13/2012 04:59 AM, Wenjing Li wrote: Dear Doug, Sorry for the late response. Thanks for your quick reply. Same errors happened for all of my data. There is an empty output file. I don't know what's going on. All the best, Wenjing On 9 August 2012 23:07, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Does this happen on all of your data sets or just this one? Did it create the output file? If so, does it have anything in it? doug On 08/09/2012 07:14 AM, Wenjing Li wrote: Hi Freesurfer experts, I want to extract time courses according to: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-July/015091.html Previous steps work fine, but memory corruption happened when I perform the command line (I have a 12 GB memory): mri_segstats --seg SUBID.feat/reg/freesurfer/aparc+aseg.nii.gz --in SUBID.feat/filtered_func_data.nii.gz --avgwf file.dat I pasted the errors below: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg /mnt/workspace/subid.feat/reg/freesurfer/aparc+aseg.nii.gz --in /mnt/workspace/subid.feat/filtered_func_data.nii.gz --avgwf /mnt/workspace/subid.feat/file.dat sysname Linux hostname fmri-Canlab machine x86_64 user wenjing Loading /mnt/workspace/subid.feat/reg/freesurfer/aparc+aseg.nii.gz Loading /mnt/workspace/subid.feat/filtered_func_data.nii.gz Voxel Volume is 70.3125 mm^3 Generating list of segmentation ids Found 109 segmentations Computing statistics for each segmentation 0 0 96808 6.80682e+06 1 2 3101 218039 tel:3101%20%20218039 2 4 59 4148.44 3 5 3 210.938 4 7 152 10687.5 tel:7%20%20%20%20152%20%2010687.5 5 8816 57375 610116 8156.25 711 62 4359.38 812114 8015.63 913 26 1828.13 1014 13 914.063 1115 30 2109.38 1216257 18070.3 1317 75 5273.44 1418 31 2179.69 1524 19 1335.94 1626 11 773.438 1728 60 4218.75 1831 12 843.75 1941 3163 222399 2043 37 2601.56 2144 3 210.938 2246155 10898.4 2347789 55476.6 2449110 7734.38 2550 65 4570.31 26 51 105 7382.82 tel:51%20%20%20%20105%20%207382.82 2752 24 1687.5 2853 75 5273.44 2954 26 1828.13 3058 9 632.813 3160 59 4148.44 3263 17 1195.31 3377 19 1335.94 34 251 12 843.75 35 252 5 351.563 36 253 5 351.563 37 254 6 421.875 38 255 15 1054.69 39 1000 38 2671.88 40 1001 57 4007.81 41 1002 34 2390.63 42 1003121 8507.82 43 1005 43 3023.44 44 1006 24 1687.5 45 1007157 11039.1 46 1008263 18492.2 47 1009170 11953.1 48 1010 35 2460.94 49 1011170 11953.1 50 1012123 8648.44 51 1013121 8507.82 52 1014 74 5203.13 53 1015265 18632.8 54 1016 38 2671.88 55 1017 55 3867.19 56 1018 64 4500 57 1019 33 2320.31 58 1020 61 4289.06 59 1021 33 2320.31 60 1022201 14132.8 61 1023 49 3445.31 62 1024236 16593.8 63 1025189 13289.1 64 1026 32 2250 65 1027256 18000 66 1028379 26648.4 67 1029214 15046.9 68 1030205 14414.1 69 1031205 14414.1 70 1032 13 914.063 71 1033 29 2039.06 72 1034 21 1476.56 73 1035104 7312.5 74 2000 37 2601.56 75 2001 58 4078.13 76 2002 24 1687.5 77 2003120 8437.5 78 2005
Re: [Freesurfer] Memory allocation problem trac-all -prior
Hi all, I think I found the problem. I reduced the number of train files in the trainlist.txt file and it ran without errors. Maybe I will need more memory to run with all train files. thanks 2012/7/16 Rui Lavrador ruilavra...@gmail.com -- Forwarded message -- From: Rui Lavrador ruilavra...@gmail.com Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask? a.y On Thu, 12 Jul 2012, Rui Lavrador wrote: Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui Lavrador 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 Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory allocation problem trac-all -prior
Hi Rui - Just keep in mind that when you're removing lines from trainlist.txt, you're removing subjects from the atlas. So instead of using a tract atlas that's based on 33 subjects, you are now using a tract atlas based on as many subjects as the lines that remain in trainlist.txt. a.y On Tue, 17 Jul 2012, Rui Lavrador wrote: Hi all, I think I found the problem. I reduced the number of train files in the trainlist.txt file and it ran without errors. Maybe I will need more memory to run with all train files. thanks 2012/7/16 Rui Lavrador ruilavra...@gmail.com -- Forwarded message -- From: Rui Lavrador ruilavra...@gmail.com Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask? a.y On Thu, 12 Jul 2012, Rui Lavrador wrote: Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui Lavrador 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Memory allocation problem trac-all -prior
-- Forwarded message -- From: Rui Lavrador ruilavra...@gmail.com Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask? a.y On Thu, 12 Jul 2012, Rui Lavrador wrote: Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui Lavrador 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 Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.com -- Rui Lavrador Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavra...@fmed.uc.pt e-mail2: ruilavra...@gmail.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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Memory allocation problem trac-all -prior
Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui Lavrador ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory allocation problem trac-all -prior
Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask? a.y On Thu, 12 Jul 2012, Rui Lavrador wrote: Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui Lavrador ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] memory allocation error with mris_register for one subject
hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory allocation error with mris_register for one subject
Hi Arno can you load that sphere file in tksurfer? And run mris_info or mris_euler_number on it? I'm wondering if it is corrupted. Bruce On Mon, 18 Jun 2012, Arno Klein wrote: hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory allocation error with mris_register for one subject
aha -- it seems that just the .sphere files, not the .pial or .white files, are corrupted. is there an easy way to generate just the .sphere files again? cheers, @rno On Mon, Jun 18, 2012 at 11:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Arno can you load that sphere file in tksurfer? And run mris_info or mris_euler_number on it? I'm wondering if it is corrupted. Bruce On Mon, 18 Jun 2012, Arno Klein wrote: hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_**template.tif OASIS-0061_MR1/surf/rh.**sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere.**.. TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno 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 Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory allocation error with mris_register for one subject
sure. The mris_sphere command line should be in the recon-all.log file in the subject's scripts dir. Either run that directly, or look at the recon-all help to figure out how to do it through recon-all cheers Bruce On Mon, 18 Jun 2012, Arno Klein wrote: aha -- it seems that just the .sphere files, not the .pial or .white files, are corrupted. is there an easy way to generate just the .sphere files again? cheers, @rno On Mon, Jun 18, 2012 at 11:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Arno can you load that sphere file in tksurfer? And run mris_info or mris_euler_number on it? I'm wondering if it is corrupted. Bruce On Mon, 18 Jun 2012, Arno Klein wrote: hello! i am able to run mris_register on all of the OASIS brain images that i have tested except for one: OAS1_0061_MR1: mris_register -curv OASIS-0061_MR1/surf/rh.sphere templates/freesurfer/rh.OASIS_template.tif OASIS-0061_MR1/surf/rh.sphere_to_OASIS_template.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from OASIS-0061_MR1/surf/rh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory the .sphere files are the same size, but i get a memory error. any idea why this might be? cheers, @rno 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] memory and bus failure
I have three scans that exit with errors that I cannot comprehend. The first two indicate memory and bus failures, so I thought maybe my computer had choked during processing, but after running again I received the same errors. The third is too cryptic for me to understand at all. Can anyone offer any advice for these? 1: BEST FITNESS (o)is 321.33384 mri =0.000 curv = 2.540 unmri = -331.493 ( f=0.00 , v=0.00 , c=2.54 , q= 5.08 ) ( f=0.00 , v=0.00 , c=2.54 , q= 5.08 ) mris_topo_fixer(58671) malloc: *** mmap(size=534511616) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRISalloc(1142113, 468): could not allocate vertices Cannot allocate memory 2: searching scale 1 Z rot 65.8 searching scale 1 Z rot 66.1 searching scale 1 Z rot 66.3 global minimum found at slice 126.0, rotations (22.40, 59.33) final transformation (x=126.0, yr=22.402, zr=59.329): 0.472 -0.860 0.194 140.992; 0.795 0.510 0.328 -83.378; -0.381 -0.000 0.925 33.641; 0.000 0.000 0.000 1.000; Bus error 3: CORRECTING DEFECT 37 (vertices=32782, convex hull=6402) normal vector of length zero at vertex 95333 with 0 faces vertex 95333 has 0 face No such file or directory signature.asc Description: Message signed with OpenPGP using GPGMail ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory allocation error with mris_register
dear doug, i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i am only having this trouble for one of the subjects. after the mri_convert workaround i am still getting the same memory allocation error. cheers, @rno On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: This is a strange problem we've been having with some mgz files that were generated during a short period of time last summer when there was a bug in the mgz writing code. What version of FS are you using? In the current dev version, this should not be a problem. A work-around is to convert the orig.mgz to itself using mri_convert in the dev environment, ie, mri_convert orig.mgz orig.mgz doug Arno Klein wrote: i get the following memory allocation error for only one out of 20 oasis subjects that i processed with freesurfer 5.1 on an ubuntu 11.10 machine with 24gb memory: mris_register -curv subjects/OAS1_0061_MR1/surf/**lh.sphere templates_freesurfer/lh.KKI_2.**tif subjects/OAS1_0061_MR1/surf/** lh.sphere_to_KKItemplate.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from subjects/OAS1_0061_MR1/surf/**lh.sphere... TAGskip: tag=1717658469, failed to calloc 1868656640 bytes! Cannot allocate memory system information: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 Debian version: wheezy/sid Kernel info: Linux 3.0.0-14-generic x86_64 cheers, @rno --**--** __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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 Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory allocation error with mris_register
Try doing it in matlab, so
a = MRIread('orig.mgz');
MRIwrite(a,'orig.mgz');
doug
Arno Klein wrote:
dear doug,
i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0.
i am only having this trouble for one of the subjects.
after the mri_convert workaround i am still getting the same memory
allocation error.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
This is a strange problem we've been having with some mgz files
that were generated during a short period of time last summer when
there was a bug in the mgz writing code. What version of FS are
you using? In the current dev version, this should not be a
problem. A work-around is to convert the orig.mgz to itself using
mri_convert in the dev environment, ie,
mri_convert orig.mgz orig.mgz
doug
Arno Klein wrote:
i get the following memory allocation error for only one out
of 20 oasis subjects that i processed with freesurfer 5.1 on
an ubuntu 11.10 machine with 24gb memory:
mris_register -curv subjects/OAS1_0061_MR1/surf/lh.sphere
templates_freesurfer/lh.KKI_2.tif
subjects/OAS1_0061_MR1/surf/lh.sphere_to_KKItemplate.reg
using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
$Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading surface from subjects/OAS1_0061_MR1/surf/lh.sphere...
TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
Cannot allocate memory
system information:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.0.0-14-generic x86_64
cheers,
@rno
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--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422
tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] memory allocation error with mris_register
dear doug,
sadly, no dice.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Try doing it in matlab, so
a = MRIread('orig.mgz');
MRIwrite(a,'orig.mgz');
doug
Arno Klein wrote:
dear doug,
i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i
am only having this trouble for one of the subjects.
after the mri_convert workaround i am still getting the same memory
allocation error.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
wrote:
This is a strange problem we've been having with some mgz files
that were generated during a short period of time last summer when
there was a bug in the mgz writing code. What version of FS are
you using? In the current dev version, this should not be a
problem. A work-around is to convert the orig.mgz to itself using
mri_convert in the dev environment, ie,
mri_convert orig.mgz orig.mgz
doug
Arno Klein wrote:
i get the following memory allocation error for only one out
of 20 oasis subjects that i processed with freesurfer 5.1 on
an ubuntu 11.10 machine with 24gb memory:
mris_register -curv subjects/OAS1_0061_MR1/surf/**lh.sphere
templates_freesurfer/lh.KKI_2.**tif
subjects/OAS1_0061_MR1/surf/**lh.sphere_to_KKItemplate.reg
using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
$Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading surface from subjects/OAS1_0061_MR1/surf/**lh.sphere...
TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
Cannot allocate memory
system information:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.0.0-14-generic x86_64
cheers,
@rno
--**--**
__**_
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mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422
tel:617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 Partners
Compliance HelpLine at
http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline.
If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] memory allocation error with mris_register
Hi Arno,
Please give these matlab commands a shot.
[v,M, mr] = load_mgh('orig.mgz');
save_mgh(v, 'orig.mgz', M, mr);
-Louis
On Fri, 20 Jan 2012, Arno Klein wrote:
dear doug,
sadly, no dice.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Try doing it in matlab, so
a = MRIread('orig.mgz');
MRIwrite(a,'orig.mgz');
doug
Arno Klein wrote:
dear doug,
i am using FS v5.1 now but ran the 20 oasis subjects through FS v5.0. i
am only having this trouble for one of the subjects.
after the mri_convert workaround i am still getting the same memory
allocation error.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
wrote:
This is a strange problem we've been having with some mgz files
that were generated during a short period of time last summer when
there was a bug in the mgz writing code. What version of FS are
you using? In the current dev version, this should not be a
problem. A work-around is to convert the orig.mgz to itself using
mri_convert in the dev environment, ie,
mri_convert orig.mgz orig.mgz
doug
Arno Klein wrote:
i get the following memory allocation error for only one out
of 20 oasis subjects that i processed with freesurfer 5.1 on
an ubuntu 11.10 machine with 24gb memory:
mris_register -curv subjects/OAS1_0061_MR1/surf/**lh.sphere
templates_freesurfer/lh.KKI_2.**tif
subjects/OAS1_0061_MR1/surf/**lh.sphere_to_KKItemplate.reg
using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
$Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading surface from subjects/OAS1_0061_MR1/surf/**lh.sphere...
TAGskip: tag=1717658469, failed to calloc 1868656640 bytes!
Cannot allocate memory
system information:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.0.0-14-generic x86_64
cheers,
@rno
--**--**
__**_
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422
tel:617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 Partners
Compliance HelpLine at
http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline.
If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs:
surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] memory allocation error with mris_register
can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file
that is the problem. Maybe your partition filled up and the sphere file
isn't complete?
On Fri, 20 Jan
2012, Arno Klein wrote:
dear doug,
sadly, no dice.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Try doing it in matlab, so
a = MRIread('orig.mgz');
MRIwrite(a,'orig.mgz');
doug
Arno Klein wrote:
dear doug,
i am using FS v5.1 now but ran the 20 oasis subjects
through FS v5.0. i am only having this trouble for
one of the subjects.
after the mri_convert workaround i am still getting
the same memory allocation error.
cheers,
@rno
On Fri, Jan 20, 2012 at 4:23 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
This is a strange problem we've been having with some mgz
files
that were generated during a short period of time last summer
when
there was a bug in the mgz writing code. What version of FS
are
you using? In the current dev version, this should not be a
problem. A work-around is to convert the orig.mgz to itself
using
mri_convert in the dev environment, ie,
mri_convert orig.mgz orig.mgz
doug
Arno Klein wrote:
i get the following memory allocation error for only one
out
of 20 oasis subjects that i processed with freesurfer 5.1
on
an ubuntu 11.10 machine with 24gb memory:
mris_register -curv subjects/OAS1_0061_MR1/surf/lh.sphere
templates_freesurfer/lh.KKI_2.tif
subjects/OAS1_0061_MR1/surf/lh.sphere_to_KKItemplate.reg
using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp
$
$Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp
$
reading surface from
subjects/OAS1_0061_MR1/surf/lh.sphere...
TAGskip: tag=1717658469, failed to calloc 1868656640
bytes!
Cannot allocate memory
system information:
FREESURFER_HOME: /usr/local/freesurfer
Build stamp:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Debian version: wheezy/sid
Kernel info: Linux 3.0.0-14-generic x86_64
cheers,
@rno
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
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Re: [Freesurfer] memory allocation error with mris_register
dear bruce, you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory error. is there any way to fix the sphere without affecting anything else? neuromorphometrics has painstakingly manually edited the freesurfer labels generated for this subject and i don't want to introduce any alterations to the meshes that they labeled. cheers, @rno On Fri, Jan 20, 2012 at 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file that is the problem. Maybe your partition filled up and the sphere file isn't complete? ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory allocation error with mris_register
you can just rerun the mris_sphere command that is in the recon-all.log (or recon-all.cmd) cheers Bruce On Fri, 20 Jan 2012, Arno Klein wrote: dear bruce, you're right -- i am able to view the pial surface, but when i try to view the spherical surface with tksurfer i get the same memory error. is there any way to fix the sphere without affecting anything else? neuromorphometrics has painstakingly manually edited the freesurfer labels generated for this subject and i don't want to introduce any alterations to the meshes that they labeled. cheers, @rno On Fri, Jan 20, 2012 at 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you load the lh.sphere in tksurfer? I'm not sure it is the mgz file that is the problem. Maybe your partition filled up and the sphere file isn't complete? ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory allocation problem with mri_robust_template
Hello,
I am having a problem with mri_robust_template using too much RAM and
causing my computers to freeze. I am using fs510. I think I would like to
try to convert the inputs to uchar as Martin suggested, but I am not sure
exactly where to do this. Would I issue this command:
For each timepoint:
mv tp1/mri/norm.mgz tp1/mri/norm.orig.mgz
mri_convert -i tp1/mri/norm.orig.mgz -o tp1/mri/norm/mgz -odt uchar
recon-all -base -tp 1 -tp 2 -all
Also, my computers have two AMD processors and 4GB of DDR RAM running at
333MHZ. I dropped them down so they each only do one job, but they are
still freezing. Besides upgrading the entire cluster to something more
current, would doubling the RAM to 8GB be worthwhile?
As always, thank you so very much!
Jeff Sadino
Mahen
Fri, 11 Feb 2011 09:16:27 -0800
To Martin,
Thanks a bunch. I haven't tested out all the recommendations, but at least I
know what's going on. If I did want to convert to uchar, how would I go
about this? Is there a function included in the Freesurfer package, or would
I have to write my own function to do so? It's not a concern, as I'm
probably not going to explore this avenue, but if I get time, I might enjoy
trying to write such a function...
Regards,
Mahen
On Wed, Feb 9, 2011 at 7:07 AM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:
Hi Mahen,
4.5 is based on flirt registration which does a pairwise registration to
the first image. Since 5.0 we use the mri_robust_template tool (as it
can ignore outlier regions and produces more accurate registrations, see
Reuter et al Neuroimage 2010 ..robust registration), but it is more
memory hungry and time consuming.
If your input images are large, it can happen that mri_robust_template
uses a lot of memory. I tested that tool in the longitudinal stream
where I successfully ran it on 10 images on a 4 gig machine (those
images are probably smaller than yours).
So you have the following options:
1. use only the best 2 input images. This has been recommended in the
past, 5 inputs are usually not improving anything (see old emails on
this list from Bruce)
2. pass the flag -flirt-motioncor to recon-all and it will revert back
to using flirt (but accuracy of the registration might suffer, since the
inputs are full head images with potentially a lot of differences in
jaw, tongue, neck, eyes, scalp and cropping planes).
Another option would be to convert the inputs to uchar and see if that
fits into the memory. They will be converted to uchar anyway in the
conform step.
Best, Martin
On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote:
Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the
first step of recon-all ('recon-all -autorecon1 -subjid ...') when
using 5 anatomical datasets (our typical load for surface
reconstruction). The problem seems to come when the third dataset is
being registered, at which point recon-all exits with the following
error message:
=
Resolution: 0
Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
malloc: *** mmap(size=921600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th
slice
Cannot allocate memory
/Users/mahen/fMRI/Surfaces/cck_kmu
\n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could
not open file
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version
10.6.0: Wed Nov 10 18:13:17 PST 2010;
root:xnu-1504.9.26~3/RELEASE_I386 i386
recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST
2011
=
My machine has 4gb of RAM, and I've ssh'd into my advisor's machine
(which has 16gb) and had the same problem.
I tryed updating the binaries for recon-all and mri_robust_template
(from
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
but the problem remained unsolved.
My advisor informs me that it is now running with version 4.5 (all 5
anatomicals); I'd still like to know what's going on. I have tried
running it on version 5 with just 2 anatomical datasets, and it works
just fine.
Here is the output of bugr:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.6.0 i386
Thanks in advance,
Mahen
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Re: [Freesurfer] : Memory and CPU Allocation?
Hi Tapsya, it looks like your data are going to require about 12G of memory due to an inefficient use of memory by selxavg when there are so many time points across a run (I've never tested it with 6570 total time points!). If you want to run this on launchpad, then you'll need to request that much memory when you launch the job. doug tap...@nmr.mgh.harvard.edu wrote: Dear FSFAST, I am using the program selxavg3-sess on 3D data for a single session (i.e. selxavg3-sess -s avml07 -analysis $ana_vol -force) and it errors out with the following message: OLS Residual Pass run 1t= 0.0 ??? Error using == unknown Out of memory. Type HELP MEMORY for your options. Error in == fast_selxavg3 at 469 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; I am using FSFAST v 5.1. My analysis uses FIR design, 6 runs in each session with 18 contrasts. I executed the program on clusters 'launchpad' (@ Martino's center) and allocated 49GB to it. My question is how much CPU and memory you recommend I should allocate? I have also attached the log file in this email. Any help is greatly appreciated! Thanks. Wishes, Tapsya ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] : Memory and CPU Allocation?
Dear FSFAST, I am using the program selxavg3-sess on 3D data for a single session (i.e. selxavg3-sess -s avml07 -analysis $ana_vol -force) and it errors out with the following message: OLS Residual Pass run 1t= 0.0 ??? Error using == unknown Out of memory. Type HELP MEMORY for your options. Error in == fast_selxavg3 at 469 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; I am using FSFAST v 5.1. My analysis uses FIR design, 6 runs in each session with 18 contrasts. I executed the program on clusters 'launchpad' (@ Martino's center) and allocated 49GB to it. My question is how much CPU and memory you recommend I should allocate? I have also attached the log file in this email. Any help is greatly appreciated! Thanks. Wishes, Tapsya SCRIPT DIR :/space/adapt/1/users/tapsya/project_AVISI/ SCRIPT EXECUTED : Analysis_GLM_Volume.csh SCRIPT EXECUTED BY : tapsya DATE EXECUTED : Wed Aug 10 14:46:38 EDT 2011 -- selxavg3-sess logfile is /autofs/space/adapt_001/users/tapsya/project_AVISI/log/selxavg3-sess-bold-FIRsm6pf2.vol-110810144638.log -- preproc-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -a FIRsm6pf2.vol -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ tapsya setenv FREESURFER_HOME /usr/local/freesurfer/stable5_1_0 setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/project_AVISI/ Linux compute-0-106.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/adapt_001/users/tapsya/project_AVISI /usr/local/freesurfer/stable5_1_0/fsfast/bin/preproc-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -a FIRsm6pf2.vol -nolog Wed Aug 10 14:46:44 EDT 2011 instem f mc 1 f fmc stc 1fmc fmc.siemens sm 1 fmc.siemens fmc.siemens.sm6 mask 1 brain avml07 Template - mktemplate-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -rlf runlist -nolog -update Session: /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07 Wed Aug 10 14:46:45 EDT 2011 Detected input format at nii avml07 Update not needed Run: 002 Wed Aug 10 14:46:46 EDT 2011 avml07 002 Update not needed Run: 003 Wed Aug 10 14:46:46 EDT 2011 avml07 003 Update not needed Run: 005 Wed Aug 10 14:46:46 EDT 2011 avml07 005 Update not needed Run: 009 Wed Aug 10 14:46:46 EDT 2011 avml07 009 Update not needed Run: 010 Wed Aug 10 14:46:47 EDT 2011 avml07 010 Update not needed Run: 011 Wed Aug 10 14:46:47 EDT 2011 avml07 011 Update not needed Wed Aug 10 14:46:47 EDT 2011 mktemplate-sess completed avml07 Mask mkbrainmask-sess -maskstem brain -fsd bold -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -rlf runlist -nolog -update /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07 Wed Aug 10 14:46:48 EDT 2011 avml07 Update not needed for session-level mask avml07 Update not needed for run 002 mask avml07 Update not needed for run 002 meanval avml07 Update not needed for run 003 mask avml07 Update not needed for run 003 meanval avml07 Update not needed for run 005 mask avml07 Update not needed for run 005 meanval avml07 Update not needed for run 009 mask avml07 Update not needed for run 009 meanval avml07 Update not needed for run 010 mask avml07 Update not needed for run 010 meanval avml07 Update not needed for run 011 mask avml07 Update not needed for run 011 meanval Wed Aug 10 14:46:52 EDT 2011 mkbrainmask-sess done avml07 Registration - register-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -dof 6 -rlf runlist -per-session -nolog -update -- register-sess logfile is /dev/null -- Wed Aug 10 14:46:53 EDT 2011 setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/project_AVISI/ cd /autofs/space/adapt_001/users/tapsya/project_AVISI /usr/local/freesurfer/stable5_1_0/fsfast/bin/register-sess -s avml07 -d /autofs/space/adapt_001/users/tapsya/project_AVISI -fsd bold -dof 6 -rlf runlist -per-session -nolog -update freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110514 Linux compute-0-106.local 2.6.18-53.1.19.el5 #1 SMP Tue Apr 22 03:01:10 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07 Wed Aug 10 14:46:53 EDT 2011 /autofs/space/adapt_001/users/tapsya/project_AVISI/avml07 Wed Aug 10 14:46:54
[Freesurfer] Memory problem with mri_glmfit
Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory problem with mri_glmfit
Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Memory problem with mri_glmfit
16 GB On 11 May 2011, at 15:24, Bruce Fischl wrote: Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory problem with mri_glmfit
do you have other stuff running? On Wed, 11 May 2011, Ed Gronenschild wrote: 16 GB On 11 May 2011, at 15:24, Bruce Fischl wrote: Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory problem with mri_glmfit
I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine. On 11 May 2011, at 15:40, Bruce Fischl wrote: do you have other stuff running? On Wed, 11 May 2011, Ed Gronenschild wrote: 16 GB On 11 May 2011, at 15:24, Bruce Fischl wrote: Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory problem with mri_glmfit
oh, yes, that's definitely not enough: 4*256*256*256*72/(1024*1024) ans = 4608 On Wed, 11 May 2011, Ed Gronenschild wrote: I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine. On 11 May 2011, at 15:40, Bruce Fischl wrote: do you have other stuff running? On Wed, 11 May 2011, Ed Gronenschild wrote: 16 GB On 11 May 2011, at 15:24, Bruce Fischl wrote: Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory problem with mri_glmfit
OK, so there's no workaround from your side? There are many empty voxels in the volumes, so as a workaround I'm going to crop the volumes and hope that they will fit in the 2GB. On 11 May 2011, at 15:51, Bruce Fischl wrote: oh, yes, that's definitely not enough: 4*256*256*256*72/(1024*1024) ans = 4608 On Wed, 11 May 2011, Ed Gronenschild wrote: I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine. On 11 May 2011, at 15:40, Bruce Fischl wrote: do you have other stuff running? On Wed, 11 May 2011, Ed Gronenschild wrote: 16 GB On 11 May 2011, at 15:24, Bruce Fischl wrote: Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory problem with mri_glmfit
It has to be float because that's what it uses internally. Can you break the volume up into slices? If so, then you can analyze each separately then combine the results back together (can't do correction for multiple comparisons though). doug On 5/11/11 10:19 AM, Bruce Fischl wrote: no easy one that springs to mind, sorry. Doug: any ideas? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: OK, so there's no workaround from your side? There are many empty voxels in the volumes, so as a workaround I'm going to crop the volumes and hope that they will fit in the 2GB. On 11 May 2011, at 15:51, Bruce Fischl wrote: oh, yes, that's definitely not enough: 4*256*256*256*72/(1024*1024) ans = 4608 On Wed, 11 May 2011, Ed Gronenschild wrote: I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine. On 11 May 2011, at 15:40, Bruce Fischl wrote: do you have other stuff running? On Wed, 11 May 2011, Ed Gronenschild wrote: 16 GB On 11 May 2011, at 15:24, Bruce Fischl wrote: Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice. We noticed the info changing y type to float that was issued. We are wondering if there is a workaround for this. Ed ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory allocation problem with mri_robust_template
To Martin,
Thanks a bunch. I haven't tested out all the recommendations, but at least I
know what's going on. If I did want to convert to uchar, how would I go
about this? Is there a function included in the Freesurfer package, or would
I have to write my own function to do so? It's not a concern, as I'm
probably not going to explore this avenue, but if I get time, I might enjoy
trying to write such a function...
Regards,
Mahen
On Wed, Feb 9, 2011 at 7:07 AM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:
Hi Mahen,
4.5 is based on flirt registration which does a pairwise registration to
the first image. Since 5.0 we use the mri_robust_template tool (as it
can ignore outlier regions and produces more accurate registrations, see
Reuter et al Neuroimage 2010 ..robust registration), but it is more
memory hungry and time consuming.
If your input images are large, it can happen that mri_robust_template
uses a lot of memory. I tested that tool in the longitudinal stream
where I successfully ran it on 10 images on a 4 gig machine (those
images are probably smaller than yours).
So you have the following options:
1. use only the best 2 input images. This has been recommended in the
past, 5 inputs are usually not improving anything (see old emails on
this list from Bruce)
2. pass the flag -flirt-motioncor to recon-all and it will revert back
to using flirt (but accuracy of the registration might suffer, since the
inputs are full head images with potentially a lot of differences in
jaw, tongue, neck, eyes, scalp and cropping planes).
Another option would be to convert the inputs to uchar and see if that
fits into the memory. They will be converted to uchar anyway in the
conform step.
Best, Martin
On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote:
Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the
first step of recon-all ('recon-all -autorecon1 -subjid ...') when
using 5 anatomical datasets (our typical load for surface
reconstruction). The problem seems to come when the third dataset is
being registered, at which point recon-all exits with the following
error message:
=
Resolution: 0
Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
malloc: *** mmap(size=921600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th
slice
Cannot allocate memory
/Users/mahen/fMRI/Surfaces/cck_kmu
\n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could
not open file
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version
10.6.0: Wed Nov 10 18:13:17 PST 2010;
root:xnu-1504.9.26~3/RELEASE_I386 i386
recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST
2011
=
My machine has 4gb of RAM, and I've ssh'd into my advisor's machine
(which has 16gb) and had the same problem.
I tryed updating the binaries for recon-all and mri_robust_template
(from
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
but the problem remained unsolved.
My advisor informs me that it is now running with version 4.5 (all 5
anatomicals); I'd still like to know what's going on. I have tried
running it on version 5 with just 2 anatomical datasets, and it works
just fine.
Here is the output of bugr:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.6.0 i386
Thanks in advance,
Mahen
___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] Memory allocation problem with mri_robust_template
Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the first
step of recon-all ('recon-all -autorecon1 -subjid ...') when using 5
anatomical datasets (our typical load for surface reconstruction). The
problem seems to come when the third dataset is being registered, at which
point recon-all exits with the following error message:
=
Resolution: 0
Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
malloc: *** mmap(size=921600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th slice
Cannot allocate memory
/Users/mahen/fMRI/Surfaces/cck_kmu
\n mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could not
open file
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version 10.6.0:
Wed Nov 10 18:13:17 PST 2010; root:xnu-1504.9.26~3/RELEASE_I386 i386
recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST 2011
=
My machine has 4gb of RAM, and I've ssh'd into my advisor's machine (which
has 16gb) and had the same problem.
I tryed updating the binaries for recon-all and mri_robust_template (from
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
but the problem remained unsolved.
My advisor informs me that it is now running with version 4.5 (all 5
anatomicals); I'd still like to know what's going on. I have tried running
it on version 5 with just 2 anatomical datasets, and it works just fine.
Here is the output of bugr:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.6.0 i386
Thanks in advance,
Mahen
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Memory allocation problem with mri_robust_template
Hi Mahen,
4.5 is based on flirt registration which does a pairwise registration to
the first image. Since 5.0 we use the mri_robust_template tool (as it
can ignore outlier regions and produces more accurate registrations, see
Reuter et al Neuroimage 2010 ..robust registration), but it is more
memory hungry and time consuming.
If your input images are large, it can happen that mri_robust_template
uses a lot of memory. I tested that tool in the longitudinal stream
where I successfully ran it on 10 images on a 4 gig machine (those
images are probably smaller than yours).
So you have the following options:
1. use only the best 2 input images. This has been recommended in the
past, 5 inputs are usually not improving anything (see old emails on
this list from Bruce)
2. pass the flag -flirt-motioncor to recon-all and it will revert back
to using flirt (but accuracy of the registration might suffer, since the
inputs are full head images with potentially a lot of differences in
jaw, tongue, neck, eyes, scalp and cropping planes).
Another option would be to convert the inputs to uchar and see if that
fits into the memory. They will be converted to uchar anyway in the
conform step.
Best, Martin
On Tue, 2011-02-08 at 23:21 +0800, Mahen wrote:
Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the
first step of recon-all ('recon-all -autorecon1 -subjid ...') when
using 5 anatomical datasets (our typical load for surface
reconstruction). The problem seems to come when the third dataset is
being registered, at which point recon-all exits with the following
error message:
=
Resolution: 0
Iteration(single-prec): 1 (subsample 200) mri_robust_template(47536)
malloc: *** mmap(size=921600) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(480, 480, 248): could not allocate 921600 bytes for 207th
slice
Cannot allocate memory
/Users/mahen/fMRI/Surfaces/cck_kmu
\n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform \n
mri_convert /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz
/Users/mahen/fMRI/Surfaces/cck_kmu/mri/orig.mgz --conform
mghRead(/Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz, -1): could
not open file
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /Users/mahen/fMRI/Surfaces/cck_kmu/mri/rawavg.mgz...
Darwin MahenWillEatYourChildren.local 10.6.0 Darwin Kernel Version
10.6.0: Wed Nov 10 18:13:17 PST 2010;
root:xnu-1504.9.26~3/RELEASE_I386 i386
recon-all -s cck_kmu exited with ERRORS at Tue Feb 8 20:50:00 CST
2011
=
My machine has 4gb of RAM, and I've ssh'd into my advisor's machine
(which has 16gb) and had the same problem.
I tryed updating the binaries for recon-all and mri_robust_template
(from
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/),
but the problem remained unsolved.
My advisor informs me that it is now running with version 4.5 (all 5
anatomicals); I'd still like to know what's going on. I have tried
running it on version 5 with just 2 anatomical datasets, and it works
just fine.
Here is the output of bugr:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
Kernel info: Darwin 10.6.0 i386
Thanks in advance,
Mahen
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] memory needed to run a freesurfer stream
Hi all, I was curious as to approximately how much memory is required to run a surface through autorecon 1 and 2, and autorecon 2 and 3. I'm running them on a new server where I have to request resources, so a ballpark figure is really all I need. Thanks! Nathan ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory needed to run a freesurfer stream
Nathan, You can find that info here: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements -- On Thu, 7 Oct 2010, Nathan Dankner wrote: Hi all, I was curious as to approximately how much memory is required to run a surface through autorecon 1 and 2, and autorecon 2 and 3. I'm running them on a new server where I have to request resources, so a ballpark figure is really all I need. Thanks! Nathan ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] memory needed to run a freesurfer stream
Nathan, For recon-all you should have at least 1GB per Core. If you use a 6-core processor you should have at least 6GB to run 6 recon-all simultaneously Given the current memory price circumstances, I would ask for at least 1.5GB per Core -- PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Thu, Oct 7, 2010 at 13:06, Allison Stevens astev...@nmr.mgh.harvard.eduwrote: Nathan, You can find that info here: https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements -- On Thu, 7 Oct 2010, Nathan Dankner wrote: Hi all, I was curious as to approximately how much memory is required to run a surface through autorecon 1 and 2, and autorecon 2 and 3. I'm running them on a new server where I have to request resources, so a ballpark figure is really all I need. Thanks! Nathan ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] memory error
Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/Linux How can I correct it ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] memory error 2
Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/Linux How can I correct it ?... I have a PC with 2.5 GB RAM, and iit is the first processing that fails with an error related to memory... Why ?... Is it really a memory problem ?... There is a tip and trick that allows me to correct it ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] memory error 2
Hi Gonzalo, look at the ?h.orig.nofix or ?h.inflated.nofix and see if there is something dramatically wrong (e.g. attached cerebellum or skull). You can also look at the filled.mgz. cheers, Bruce On Tue, 24 Nov 2009, Gonzalo Rojas Costa wrote: Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/Linux How can I correct it ?... I have a PC with 2.5 GB RAM, and iit is the first processing that fails with an error related to memory... Why ?... Is it really a memory problem ?... There is a tip and trick that allows me to correct it ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] memory requirement...
Hi: I installed Freesurfer v4.4.0 in a PC with 1 GB RAM... There will be any problem to run Freesurfer in that PC, or only it runs slow ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] memory alloc problem in mri_fwhm
Hi, I am analyzing my fMRI data and I got a memory alloc problem in mri_fwhm The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from freesurfer-Linux-rh9-stable-pub-v4.0.5. I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] memory alloc problem in mri_fwhm
how big is all.nii and how much memory do you have on that computer? Krishna Srihasam wrote: Hi, I am analyzing my fMRI data and I got a memory alloc problem in mri_fwhm The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from freesurfer-Linux-rh9-stable-pub-v4.0.5. I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] memory alloc problem in mri_fwhm
Hi, all.nii takes 1309 MB. I have 4 GB RAM and a 80 GB HDD. regards, Krishna Douglas N Greve wrote: how big is all.nii and how much memory do you have on that computer? Krishna Srihasam wrote: Hi, I am analyzing my fMRI data and I got a memory alloc problem in mri_fwhm The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from freesurfer-Linux-rh9-stable-pub-v4.0.5. I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] memory alloc problem in mri_fwhm
that's probably the problem then, since mri_fwhm will need about 6x the size of all.nii. Run selxavg3-sess with the -no-fwhm option (though it might not be in your version). Krishna Srihasam wrote: Hi, all.nii takes 1309 MB. I have 4 GB RAM and a 80 GB HDD. regards, Krishna Douglas N Greve wrote: how big is all.nii and how much memory do you have on that computer? Krishna Srihasam wrote: Hi, I am analyzing my fMRI data and I got a memory alloc problem in mri_fwhm The exact message is : mri_fwhm --mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii --i /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/res/all.nii --sum /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.sum --dat /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/fwhm.dat MRIalloc(96, 84, 33): could not allocate 32256 bytes for 12483th slice voxelvolume 3.1901 mm3 Loading mask /tmp/sk/FSFAST/abe_090116/bold/VisualActivations/mask.nii Search region is 84788 voxels = 270482.522603 mm3 Polynomial detrending, order = 0 Detrending Cannot allocate memory I am using the binaries from freesurfer-Linux-rh9-stable-pub-v4.0.5. I am pretty new to FSFAST. Any pointers will be helpful. regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Memory Problem when running mris_volmask
Hello, When I run the command mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1 I get the following error: ERROR: opening pipe gzip -f -c /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas? Thanks a lot, Javier. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory Problem when running mris_volmask
Javier, It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly). Nick On Wed, 2008-03-05 at 10:28 -0500, [EMAIL PROTECTED] wrote: Hello, When I run the command mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1 I get the following error: ERROR: opening pipe gzip -f -c /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas? Thanks a lot, Javier. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory Problem when running mris_volmask
Hi Nick, I checked disk space and there are still 59G available, so that should not be the problem. About RAM this system has 3GB. Any idea of what might be going on? Thanks a lot, Javier. Quoting Nick Schmansky [EMAIL PROTECTED]: Javier, It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly). Nick On Wed, 2008-03-05 at 10:28 -0500, [EMAIL PROTECTED] wrote: Hello, When I run the command mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1 I get the following error: ERROR: opening pipe gzip -f -c /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas? Thanks a lot, Javier. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory Problem when running mris_volmask
Javier, Which gzip version is being used? (gzip --version) Nick On Wed, 2008-03-05 at 11:54 -0500, [EMAIL PROTECTED] wrote: Hi Nick, I checked disk space and there are still 59G available, so that should not be the problem. About RAM this system has 3GB. Any idea of what might be going on? Thanks a lot, Javier. Quoting Nick Schmansky [EMAIL PROTECTED]: Javier, It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly). Nick On Wed, 2008-03-05 at 10:28 -0500, [EMAIL PROTECTED] wrote: Hello, When I run the command mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1 I get the following error: ERROR: opening pipe gzip -f -c /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas? Thanks a lot, Javier. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory Problem when running mris_volmask
The output of gzip --version is: gzip 1.3.12 Copyright (C) 2007 Free Software Foundation, Inc. Copyright (C) 1993 Jean-loup Gailly. This is free software. You may redistribute copies of it under the terms of the GNU General Public License http://www.gnu.org/licenses/gpl.html. There is NO WARRANTY, to the extent permitted by law. Written by Jean-loup Gailly. Javier. Quoting Nick Schmansky [EMAIL PROTECTED]: Javier, Which gzip version is being used? (gzip --version) Nick On Wed, 2008-03-05 at 11:54 -0500, [EMAIL PROTECTED] wrote: Hi Nick, I checked disk space and there are still 59G available, so that should not be the problem. About RAM this system has 3GB. Any idea of what might be going on? Thanks a lot, Javier. Quoting Nick Schmansky [EMAIL PROTECTED]: Javier, It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly). Nick On Wed, 2008-03-05 at 10:28 -0500, [EMAIL PROTECTED] wrote: Hello, When I run the command mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1 I get the following error: ERROR: opening pipe gzip -f -c /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas? Thanks a lot, Javier. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory Problem when running mris_volmask
Hi Nick, After a long morning of looking through everything that was running on the computer, I finally made it work after: (1) Stopping some of the processes that were taking more memory. (2) Cleaning some stuff on the / filesystem. In fact I think this second point might have been the biggest issue. Although the drive where the data is written has 57G of free space, the / filesystem had only 1.5G free. I do not know if freesurfer might try to temporarily write things in there (such as /tmp), and that migth have been the problem. The truth is that after making the / filesystem go back to 5G of free space the command mris_volmask run with no problems until the end. Thanks a lot for your help, I really, really appreciate the quick response you had this morning. Have a good day, Javier. Quoting Nick Schmansky [EMAIL PROTECTED]: Javier, Does mri_convert output .mgz files? What OS is being used? If mri_convert doesnt produce .mgz files, then I don't know what to suggest. Nick On Wed, 2008-03-05 at 12:22 -0500, [EMAIL PROTECTED] wrote: The output of gzip --version is: gzip 1.3.12 Copyright (C) 2007 Free Software Foundation, Inc. Copyright (C) 1993 Jean-loup Gailly. This is free software. You may redistribute copies of it under the terms of the GNU General Public License http://www.gnu.org/licenses/gpl.html. There is NO WARRANTY, to the extent permitted by law. Written by Jean-loup Gailly. Javier. Quoting Nick Schmansky [EMAIL PROTECTED]: Javier, Which gzip version is being used? (gzip --version) Nick On Wed, 2008-03-05 at 11:54 -0500, [EMAIL PROTECTED] wrote: Hi Nick, I checked disk space and there are still 59G available, so that should not be the problem. About RAM this system has 3GB. Any idea of what might be going on? Thanks a lot, Javier. Quoting Nick Schmansky [EMAIL PROTECTED]: Javier, It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly). Nick On Wed, 2008-03-05 at 10:28 -0500, [EMAIL PROTECTED] wrote: Hello, When I run the command mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1 I get the following error: ERROR: opening pipe gzip -f -c /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, errno = 12 Cannot allocate memory mghWrite(/home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz, -1): could not open file I had this error on a previous step and managed to solve it by means of using directories with COR files instead of a single mgz file for input and output. I do not see any option in mris_volmask to force it to write each COR file independently instead of a single .mgz file. How can I do this so I do not run into a memory problem? Also, any other ideas? Thanks a lot, Javier. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory problems
This is not a compiled program (it is a script). You may need to have a sys admin look at it. doug Juergen Haenggi wrote: Hi Doug I tried to make that file executable (as root I typed chmod a+x make_average_volume) but it did not work. The file I found under the URL you send me is a text file and it is not compiled. Please can you give me any hint to make the new version of make_average_volume executable. Is there a compiled version that is already executable? Thanks a lot in advance Best regards Juergen On 4.1.2008 23:06 Uhr, Doug Greve [EMAIL PROTECTED] wrote: You may have to make it executable Juergen Haenggi wrote: Hi Doug Thanks for the new version, but the following error occurred: Cleaning up --- rm -r ./tmp.mris_preproc.9682 Fri Jan 4 21:36:04 CET 2008 mris_preproc done --- Fri Jan 4 21:36:04 CET 2008 make_average_surface done make_average_volume --subjects SNPs_Vp01 SNPs_Vp02 SNPs_Vp03 SNPs_Vp04 SNPs_Vp05 SNPs_Vp06 SNPs_Vp07 SNPs_Vp08 SNPs_Vp09 SNPs_Vp10 SNPs_Vp11 SNPs_Vp12 SNPs_Vp13 SNPs_Vp14 SNPs_Vp15 SNPs_Vp16 SNPs_Vp17 SNPs_Vp18 SNPs_Vp19 SNPs_Vp20 SNPs_Vp21 SNPs_Vp22 SNPs_Vp23 SNPs_Vp24 SNPs_Vp25 SNPs_Vp26 SNPs_Vp27 SNPs_Vp28 SNPs_Vp29 SNPs_Vp30 SNPs_Vp31 SNPs_Vp32 SNPs_Vp33 SNPs_Vp34 SNPs_Vp35 SNPs_Vp36 SNPs_Vp37 SNPs_Vp38 SNPs_Vp39 SNPs_Vp40 SNPs_Vp41 SNPs_Vp42 SNPs_Vp43 SNPs_Vp44 SNPs_Vp45 SNPs_Vp46 SNPs_Vp47 SNPs_Vp48 SNPs_Vp49 SNPs_Vp50 SNPs_Vp51 SNPs_Vp52 SNPs_Vp53 SNPs_Vp54 SNPs_Vp55 SNPs_Vp56 SNPs_Vp57 SNPs_Vp58 SNPs_Vp59 SNPs_Vp60 SNPs_Vp61 SNPs_Vp62 SNPs_Vp63 SNPs_Vp64 SNPs_Vp65 SNPs_Vp66 SNPs_Vp67 SNPs_Vp68 SNPs_Vp69 SNPs_Vp70 SNPs_Vp71 SNPs_Vp72 SNPs_Vp73 SNPs_Vp74 SNPs_Vp75 SNPs_Vp76 SNPs_Vp77 SNPs_Vp78 SNPs_Vp79 SNPs_Vp80 SNPs_Vp81 SNPs_Vp82 SNPs_Vp83 SNPs_Vp84 SNPs_Vp85 SNPs_Vp86 SNPs_Vp87 SNPs_Vp88 SNPs_Vp89 SNPs_Vp90 SNPs_Vp91 SNPs_Vp92 'csh: Unknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] juergenh% Best regards Juergen On 3.1.2008 21:03 Uhr, Doug Greve [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: This is a problem when it attempts to create an average aseg. As a stop-gap measure, I've created a new version that will not stop the execution if this stage fails. You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_vol ume doug Juergen Haenggi, Psychological Institute wrote: Dear FS experts I tried to average the brains of 92 subjects. We used a MacPro Quad with 5 GB RAM and about 10 GB virtual memory. When running make_average_subject the following error occurred: Checking 91 /Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs_V p92.mgh nframestot = 92 Allocing output mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error code=3) mri_concat(13587) malloc: *** error: can't allocate region mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th slice Cannot allocate memory [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] juergenh% Does it really mean there is too less memory or is it a similar problem occurred in other software, i.e. memory acquisition restriction by the Java Runtime Environment? Is there any possibility, beside buying more RAM, to run make_average_subject with the available 5 GB RAM? Thanks in advance and Happy New Year Best regards Juergen - Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone
Re: [Freesurfer] Memory problems
Hi Doug I tried to make that file executable (as root I typed chmod a+x make_average_volume) but it did not work. The file I found under the URL you send me is a text file and it is not compiled. Please can you give me any hint to make the new version of make_average_volume executable. Is there a compiled version that is already executable? Thanks a lot in advance Best regards Juergen On 4.1.2008 23:06 Uhr, Doug Greve [EMAIL PROTECTED] wrote: You may have to make it executable Juergen Haenggi wrote: Hi Doug Thanks for the new version, but the following error occurred: Cleaning up --- rm -r ./tmp.mris_preproc.9682 Fri Jan 4 21:36:04 CET 2008 mris_preproc done --- Fri Jan 4 21:36:04 CET 2008 make_average_surface done make_average_volume --subjects SNPs_Vp01 SNPs_Vp02 SNPs_Vp03 SNPs_Vp04 SNPs_Vp05 SNPs_Vp06 SNPs_Vp07 SNPs_Vp08 SNPs_Vp09 SNPs_Vp10 SNPs_Vp11 SNPs_Vp12 SNPs_Vp13 SNPs_Vp14 SNPs_Vp15 SNPs_Vp16 SNPs_Vp17 SNPs_Vp18 SNPs_Vp19 SNPs_Vp20 SNPs_Vp21 SNPs_Vp22 SNPs_Vp23 SNPs_Vp24 SNPs_Vp25 SNPs_Vp26 SNPs_Vp27 SNPs_Vp28 SNPs_Vp29 SNPs_Vp30 SNPs_Vp31 SNPs_Vp32 SNPs_Vp33 SNPs_Vp34 SNPs_Vp35 SNPs_Vp36 SNPs_Vp37 SNPs_Vp38 SNPs_Vp39 SNPs_Vp40 SNPs_Vp41 SNPs_Vp42 SNPs_Vp43 SNPs_Vp44 SNPs_Vp45 SNPs_Vp46 SNPs_Vp47 SNPs_Vp48 SNPs_Vp49 SNPs_Vp50 SNPs_Vp51 SNPs_Vp52 SNPs_Vp53 SNPs_Vp54 SNPs_Vp55 SNPs_Vp56 SNPs_Vp57 SNPs_Vp58 SNPs_Vp59 SNPs_Vp60 SNPs_Vp61 SNPs_Vp62 SNPs_Vp63 SNPs_Vp64 SNPs_Vp65 SNPs_Vp66 SNPs_Vp67 SNPs_Vp68 SNPs_Vp69 SNPs_Vp70 SNPs_Vp71 SNPs_Vp72 SNPs_Vp73 SNPs_Vp74 SNPs_Vp75 SNPs_Vp76 SNPs_Vp77 SNPs_Vp78 SNPs_Vp79 SNPs_Vp80 SNPs_Vp81 SNPs_Vp82 SNPs_Vp83 SNPs_Vp84 SNPs_Vp85 SNPs_Vp86 SNPs_Vp87 SNPs_Vp88 SNPs_Vp89 SNPs_Vp90 SNPs_Vp91 SNPs_Vp92 'csh: Unknown option: `- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] juergenh% Best regards Juergen On 3.1.2008 21:03 Uhr, Doug Greve [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: This is a problem when it attempts to create an average aseg. As a stop-gap measure, I've created a new version that will not stop the execution if this stage fails. You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_v ol ume doug Juergen Haenggi, Psychological Institute wrote: Dear FS experts I tried to average the brains of 92 subjects. We used a MacPro Quad with 5 GB RAM and about 10 GB virtual memory. When running make_average_subject the following error occurred: Checking 91 /Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs _V p92.mgh nframestot = 92 Allocing output mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error code=3) mri_concat(13587) malloc: *** error: can't allocate region mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th slice Cannot allocate memory [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] juergenh% Does it really mean there is too less memory or is it a similar problem occurred in other software, i.e. memory acquisition restriction by the Java Runtime Environment? Is there any possibility, beside buying more RAM, to run make_average_subject with the available 5 GB RAM? Thanks in advance and Happy New Year Best regards Juergen - Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) --- --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich
[Freesurfer] Memory problems
Dear FS experts I tried to average the brains of 92 subjects. We used a MacPro Quad with 5 GB RAM and about 10 GB virtual memory. When running make_average_subject the following error occurred: Checking 91 /Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs_Vp92.mgh nframestot = 92 Allocing output mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error code=3) mri_concat(13587) malloc: *** error: can't allocate region mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th slice Cannot allocate memory [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] juergenh% Does it really mean there is too less memory or is it a similar problem occurred in other software, i.e. memory acquisition restriction by the Java Runtime Environment? Is there any possibility, beside buying more RAM, to run make_average_subject with the available 5 GB RAM? Thanks in advance and Happy New Year Best regards Juergen - Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Memory problems
Hi Juergen, can you send us the full command line and version info? thanks (and happy new year!) Bruce On Tue, 1 Jan 2008, Juergen Haenggi, Psychological Institute wrote: Dear FS experts I tried to average the brains of 92 subjects. We used a MacPro Quad with 5 GB RAM and about 10 GB virtual memory. When running make_average_subject the following error occurred: Checking 91 /Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs_Vp92.mgh nframestot = 92 Allocing output mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error code=3) mri_concat(13587) malloc: *** error: can't allocate region mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th slice Cannot allocate memory [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] juergenh% Does it really mean there is too less memory or is it a similar problem occurred in other software, i.e. memory acquisition restriction by the Java Runtime Environment? Is there any possibility, beside buying more RAM, to run make_average_subject with the available 5 GB RAM? Thanks in advance and Happy New Year Best regards Juergen - Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL PROTECTED] (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] memory limitations
Running recon-all with the v3.0.2 release, I have noticed recently that the process will run into seg faults at various stages (e.g. topology correction, sphere reg, or cortical parcellation). This seems somewhat random, but judging from some other posts, and the fact that it happenened when I was running multiple jobs at once but didn't (for the same subject) when it was the only job, it seems to be memory dependent. That is, when there is not enough available memory, things crash without warning or relevant error messages (e.g. not enough memory). Does that seem like an accurate assessment of things? Aside from hardware solutions (e.g. more RAM or bigger swap space), is there anything that can be done to the software to allow the user to balance speed with memory usage? And die in a less mysterious way? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] memory limitations
Hi Don, we certainly try to trap all memory allocation failures, but no doubt have missed a few. We'll try to track them down, but in the meantime you're better of running things in series since it won't run any faster anyway, and this way it will stop failing :) Bruce On Sun, 4 Jun 2006, Don Hagler wrote: Running recon-all with the v3.0.2 release, I have noticed recently that the process will run into seg faults at various stages (e.g. topology correction, sphere reg, or cortical parcellation). This seems somewhat random, but judging from some other posts, and the fact that it happenened when I was running multiple jobs at once but didn't (for the same subject) when it was the only job, it seems to be memory dependent. That is, when there is not enough available memory, things crash without warning or relevant error messages (e.g. not enough memory). Does that seem like an accurate assessment of things? Aside from hardware solutions (e.g. more RAM or bigger swap space), is there anything that can be done to the software to allow the user to balance speed with memory usage? And die in a less mysterious way? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
