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 . 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. > _______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
