External Email - Use Caution Dear freesurfer experts, I found the same problems with recon-all (segmentation failure) using a Mac OS Sierra (10.12) and the same failures (more than 10% of cases) with the command: recon-all -base template -tp subj001 -tp subj002 -all
Hope it is possible to find a solution Thank you Angela > Il giorno 30 mag 2020, alle ore 12:47, Angela Favaro <angela.fav...@unipd.it> > ha scritto: > > External Email - Use Caution > > > Dear Freesurfer experts, > I continued to go on with my data set using 7.1.0 (with a Catalina MacOS > 10.15) and in more than 10% of subjects recon-all -all failed. > Failures were always at the segmentation stage (as I showed you in a previous > mail) and all these subjects were processed without errors using Freesurfer > 6. > What do you think is the problem and do you have any suggestion on how to > overcome it? > Thank you > > Angela > >> Il giorno 28 mag 2020, alle ore 23:18, Angela Favaro <angela.fav...@unipd.it >> <mailto:angela.fav...@unipd.it>> ha scritto: >> >> External Email - Use Caution >> >> >> Thank you! >> >> >>> Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew >>> <ahoo...@mgh.harvard.edu <mailto:ahoo...@mgh.harvard.edu>> ha scritto: >>> >>> Hi Angela, >>> >>> This is a bug on osx, which does not have the --preserve=timestamps flag >>> available to cp. This will be fixed in the next 7.1 patch, but in the >>> meantime, you can fix this manually via: >>> >>> cd $FREESURFER_HOME/bin >>> sudo rm rca-long-tp-init >>> sudo curl >>> https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init >>> >>> <https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init> >>> -o rca-long-tp-init >>> sudo chmod +x rca-long-tp-init >>> >>> Best >>> Andrew >>> >>> >>> From: <freesurfer-boun...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Angela Favaro >>> <angela.fav...@unipd.it <mailto:angela.fav...@unipd.it>> >>> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Date: Wednesday, May 27, 2020 at 4:27 PM >>> To: FS Help <freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Subject: [Freesurfer] Problems with freesurfer 7.1.0 >>> >>> External Email - Use Caution >>> Dear Freesurfer experts, >>> I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a >>> McOS Catalina. I found 2 main problems >>> 1. About a 10% of cases failed at the segmentation stage during the >>> recon-all processing (I uploaded one of these cases in one of my previous >>> mails) >>> 2. After the building of the template during the longitudinal processing, >>> at the recon-all -long I found the following error: >>> >>> >>>> longmc Done >>>> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri >>>> \n cp -f --preserve=timestamps >>>> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz >>>> ./brainmask_template4.mgz \n >>>> cp: illegal option -- - >>>> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file >>>> cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... >>>> target_directory >>>> ERROR: >>>> Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct >>>> 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64 >>> >>> >>>> recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 >>>> 03:47:31 CEST 2020 >>>> >>>> >>> >>> >>> Can you please help me with this two issues? >>> Thank you so much! >>> >>> Angela >>> >>> >>> >>> >>> >>>> Inizio messaggio inoltrato: >>>> >>>> Da: Angela Favaro <angela.fav...@unipd.it <mailto:angela.fav...@unipd.it>> >>>> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 >>>> Data: 23 maggio 2020 10:41:02 CEST >>>> A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>> Rispondi a: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>> >>>> External Email - Use Caution >>>> >>>> Dear Freesurfer experts, >>>> I am trying to process a dataset with a longitudinal design. >>>> However, after building the template, at the “recon-all -long” command I >>>> got this error: >>>> >>>> longmc Done >>>> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri >>>> \n cp -f --preserve=timestamps >>>> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz >>>> ./brainmask_template4.mgz \n >>>> cp: illegal option -- - >>>> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file >>>> cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... >>>> target_directory >>>> ERROR: >>>> Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct >>>> 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64 >>>> >>>> recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 >>>> 03:47:31 CEST 2020 >>>> >>>> For more details, see the log file >>>> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log >>>> >>>> >>>> >>>> >>>> Thank you for any help! >>>> >>>> >>>> Angela >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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
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