External Email - Use Caution
Hello,
I am getting a strange message when trying to run the amygdala and hippocampal sementations, even when attempting to run the script on someone who the script previously completed.
When it starts, the script immediately displays the following message:
error parsing license file, expected 4 values
The license error message further instructs libc requires a newly formatted license so I got a new one. The new one is identical to the original however and it has four entries - my email address, a five digit number, followed by two alphanumeric strings..
The script then seems to start, will run for about 30 seconds or so then stop again with the following message:
Error using segmentSubjectT1_autoEstimateAlveusML (line 533) Fitting mesh to synthetic image resulted in no deformation
...
T1 hippocampal subfields exited with ERRORS at Thu Dec 3 15:56:32 MST 2020
I get slightly different errors when running on another subject, who like the one above, previously completed. For this subject the license error is more persistent:
error parsing license file, expected 4 values
I've attached the hippocampal-subfields-T1.log for the first subject as it contains the full output. Thank you, Keith
Dear Keith, It is a license problem. The hippo/amygdala module relies on mri_robust_register for initialization, and this program is failing due to the aforementioned license problem. Once that has been fixed, the hippocampal module should be fine. Regarding the license problem: I have no idea, but I am CCing Andrew Hoopes, who hopefully will be able to help. Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Keith Harenski kharenski@mrn.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, December 4, 2020 at 16:24 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T1.sh failing {Disarmed}
External Email - Use Caution Hello,
I am getting a strange message when trying to run the amygdala and hippocampal sementations, even when attempting to run the script on someone who the script previously completed.
When it starts, the script immediately displays the following message: error parsing license file, expected 4 values
The license error message further instructs libc requires a newly formatted license so I got a new one. The new one is identical to the original however and it has four entries - my email address, a five digit number, followed by two alphanumeric strings..
The script then seems to start, will run for about 30 seconds or so then stop again with the following message: Error using segmentSubjectT1_autoEstimateAlveusML (line 533) Fitting mesh to synthetic image resulted in no deformation ... T1 hippocampal subfields exited with ERRORS at Thu Dec 3 15:56:32 MST 2020
I get slightly different errors when running on another subject, who like the one above, previously completed. For this subject the license error is more persistent: error parsing license file, expected 4 values
I've attached the hippocampal-subfields-T1.log for the first subject as it contains the full output. Thank you, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory
The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office (Cell): 505.504.1338 | Fax: 505.272.8002 kharenski@mrn.orgmailto:kharenski@mrn.org | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.mrn.orghttp://secure-web.cisco.com/1dteY9vqOnPkmed6Gi9ngcVDCP_LkM_NDWWJ44EjsUH1kpcdY7pTUt_OAitzF2jiVojEqlNmU6ChusO7dxvMmEwotJUObbbe7vs_DFHynWzqHzC3LWZf93olez5aVnSRCPR5TQoWwmBkjKr3XecflF6yGRSp8YtB-6q8n75jHWlh-Ia_WT6aJwFYFvv_tBlbcyp10DxHmwim-6ges_U8rNZSuQyymAV76fqRkx4n0WnPWCD30Z5D1QGMs_5OcL9GypONAcMJvHD-sd7CzPfMNLA/http%3A%2F%2Fwww.mrn.org | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.lrri.orghttp://secure-web.cisco.com/1IdoCx7NC76tQWgH2bVZIQ__Bemn520Wpm_zpCLpupf-KHJkvcBLwX074rPgBz2xPoFAlur--Bkoal8s61dCB_nLzQeVx2eAByAA90x4sUMBSU6lfJb4otMWNUAZCS5mamQTHJWTSLXPSI6aa1B7ffLiv_BX6zpQNRdSsu3yb_QE59Wa3Srj6lksD5Zxc5DpOkvRgaCo3UwoUinkXyeiyReXIpvNXAq_sYXQaLhHJGwSlMczlqOv8yMtvKNrjVYbHk8-z5nibeIRSk70qufpgnA/http%3A%2F%2Fwww.lrri.org
Hi Keith, what version of ubuntu are you using?
Best Andrew
From: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu Date: Friday, December 4, 2020 at 4:42 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Cc: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] segmentHA_T1.sh failing {Disarmed}
Dear Keith, It is a license problem. The hippo/amygdala module relies on mri_robust_register for initialization, and this program is failing due to the aforementioned license problem. Once that has been fixed, the hippocampal module should be fine. Regarding the license problem: I have no idea, but I am CCing Andrew Hoopes, who hopefully will be able to help. Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Keith Harenski kharenski@mrn.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, December 4, 2020 at 16:24 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T1.sh failing {Disarmed}
External Email - Use Caution Hello,
I am getting a strange message when trying to run the amygdala and hippocampal sementations, even when attempting to run the script on someone who the script previously completed.
When it starts, the script immediately displays the following message: error parsing license file, expected 4 values
The license error message further instructs libc requires a newly formatted license so I got a new one. The new one is identical to the original however and it has four entries - my email address, a five digit number, followed by two alphanumeric strings..
The script then seems to start, will run for about 30 seconds or so then stop again with the following message: Error using segmentSubjectT1_autoEstimateAlveusML (line 533) Fitting mesh to synthetic image resulted in no deformation ... T1 hippocampal subfields exited with ERRORS at Thu Dec 3 15:56:32 MST 2020
I get slightly different errors when running on another subject, who like the one above, previously completed. For this subject the license error is more persistent: error parsing license file, expected 4 values
I've attached the hippocampal-subfields-T1.log for the first subject as it contains the full output. Thank you, Keith -- Keith Harenski Mobile MRI Manager Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory
The Mind Research Network 1101 Yale Blvd NE Albuquerque, NM 87106-4188 Office (Cell): 505.504.1338 | Fax: 505.272.8002 kharenski@mrn.orgmailto:kharenski@mrn.org | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.mrn.orghttp://secure-web.cisco.com/1dteY9vqOnPkmed6Gi9ngcVDCP_LkM_NDWWJ44EjsUH1kpcdY7pTUt_OAitzF2jiVojEqlNmU6ChusO7dxvMmEwotJUObbbe7vs_DFHynWzqHzC3LWZf93olez5aVnSRCPR5TQoWwmBkjKr3XecflF6yGRSp8YtB-6q8n75jHWlh-Ia_WT6aJwFYFvv_tBlbcyp10DxHmwim-6ges_U8rNZSuQyymAV76fqRkx4n0WnPWCD30Z5D1QGMs_5OcL9GypONAcMJvHD-sd7CzPfMNLA/http%3A%2F%2Fwww.mrn.org | MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.lrri.orghttp://secure-web.cisco.com/1IdoCx7NC76tQWgH2bVZIQ__Bemn520Wpm_zpCLpupf-KHJkvcBLwX074rPgBz2xPoFAlur--Bkoal8s61dCB_nLzQeVx2eAByAA90x4sUMBSU6lfJb4otMWNUAZCS5mamQTHJWTSLXPSI6aa1B7ffLiv_BX6zpQNRdSsu3yb_QE59Wa3Srj6lksD5Zxc5DpOkvRgaCo3UwoUinkXyeiyReXIpvNXAq_sYXQaLhHJGwSlMczlqOv8yMtvKNrjVYbHk8-z5nibeIRSk70qufpgnA/http%3A%2F%2Fwww.lrri.org
freesurfer@nmr.mgh.harvard.edu
-
Hoopes, Andrew -
Iglesias Gonzalez, Juan E. -
Keith Harenski