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 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 _______________________________________________ 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
