Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Eugenio, I have a question about hippocampal segmentation. Do you think it is possible to use this segmentation to obtain specific seeds for a functional connectivity study? thank you Angela Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Angela, Of course it is! I'd be thrilled to see what you get out of your analyses; please keep me posted. 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 13, 2015 11:21:30 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi Eugenio, I have a question about hippocampal segmentation. Do you think it is possible to use this segmentation to obtain specific seeds for a functional connectivity study? thank you Angela Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
thanks, that solved my problem! Angela Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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 hippocampal-subfields-T1.log Description: Binary data ___ 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] FS Developer v6 Hippocampal Segmentation
Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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 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. run_segmentSubjectT1_autoEstimateAlveusML.sh Description: application/shellscript run_segmentSubjectT1T2_autoEstimateAlveusML.sh Description: application/shellscript run_segmentSubjectT2_autoEstimateAlveusML.sh Description: application/shellscript ___ 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] FS Developer v6 Hippocampal Segmentation
Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi all, I am also running hippocampal subfields segmentation with V6 develop version, and I got the error as following: # #@# Hippocampal Subfields processing (T1 only) left Tue Jun 30 23:06:21 PDT 2015 /home/xzhuang/Downloads/freesurfer/bin/segmentSF_T1.sh /home/xzhuang/Downloads/freesurfer/MCRv80 /home/xzhuang/Downloads/freesurfer 1 /home/xzhuang/Downloads/freesurfer/subjects left See log file: /home/xzhuang/Downloads/freesurfer/subjects/1/scripts/hippocampal-subfields-T1.log Linux localhost.localdomain 3.10.0-123.8.1.el7.x86_64 #1 SMP Mon Sep 22 19:06:58 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1 exited with ERRORS at Tue Jun 30 23:06:21 PDT 2015 For more details, see the log file /home/xzhuang/Downloads/freesurfer/subjects/1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting; And inside log file is following: # #@# Hippocampal Subfields processing (T1 only) left Tue Jun 30 23:06:21 PDT 2015 Is there any suggestions, thoughts or similar experience? Best, Xiaowei. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, July 1, 2015 4:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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 - Original Message - From: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/ange lafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelaf avaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/D esktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data
[Freesurfer] FS Developer v6 Hippocampal Segmentation
Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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] FS Developer v6 Hippocampal Segmentation
Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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 - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
