Re: [Freesurfer] -hippocampal-subfields-T1T2
Hi All, Was this issue solved?? I am getting the similar error but couldn't find a solution on the mailing list. Fitting mesh to synthetic image from ASEG took 362.0884 seconds Transforming points Transforming points set final LTA type to 1 ltaReadFile(subject/mri/transforms/T1_to_T2.v10.lta): can't open file No such file or directory Segmentation fault (core dumped) freesurfer/bin//mri_concatenate_lta -out_type 1 subject/mri/transforms/T1_to_T2.v10.lta identity.nofile T1toT2.lta >/dev/null: Segmentation fault Error using fgets Invalid file identifier. Use fopen to generate a valid file identifier. Regards, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Eugenio Iglesias <e.igles...@bcbl.eu> Sent: Monday, October 19, 2015 8:59:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] -hippocampal-subfields-T1T2 Hi Daniel, sorry for the late reply; I was on vacation. It seems that the T1-T2 registration failed. Can you please send me the .log files for the hippocampal subfields? They should be in the following directory: media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/scripts/ Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Daniele Orlandi" <daniele.orlandi@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, October 12, 2015 6:58:34 PM Subject: [Freesurfer] -hippocampal-subfields-T1T2 Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): > can't open file >No such file or directory >ERROR: Reading transform from file >/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele ___ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563<tel:%2B39%20030%2F3501563> cell: +39 3495119685 <tel:%2B39%20030%2F3501563> email: dorla...@fatebenefratelli.it<mailto:dorla...@fatebenefratelli.it>; daniele.orlandi@gmail.com<mailto:daniele.orlandi@gmail.com> (http://www.centroalzheimer.org/sito/chi_staff_e.php) ___ 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.
Re: [Freesurfer] -hippocampal-subfields-T1T2
Hi Daniel, sorry for the late reply; I was on vacation. It seems that the T1-T2 registration failed. Can you please send me the .log files for the hippocampal subfields? They should be in the following directory: media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/scripts/ Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Daniele Orlandi" <daniele.orlandi@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, October 12, 2015 6:58:34 PM Subject: [Freesurfer] -hippocampal-subfields-T1T2 Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): > can't open file >No such file or directory >ERROR: Reading transform from file >/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta > Do you have any suggestion? thank you all for your collaboration Daniele ___ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel: +39 030/3501563 cell: +39 3495119685 email: dorla...@fatebenefratelli.it ; daniele.orlandi@gmail.com ( http://www.centroalzheimer.org/sito/chi_staff_e.php ) ___ 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] -hippocampal-subfields-T1T2
Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): can't open file >No such file or directory >ERROR: Reading transform from file /media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele ___ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorla...@fatebenefratelli.it; daniele.orlandi@gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php) ___ 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.
