You need to provide input data for the subject. This would either go in the 150622fracal/mri/orig folder or use the -i flag to point to the input file.
-Zeke > After this command > recon-all -all -s 150622fracal -hippocampal-subfields-T1 > > this error come out: > > Applications/freesurfer/subjects/150622fracal/scripts/recon-all.log > Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue > Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 > Can't locate MNI/Startup.pm in @INC (you may need to install the MNI:: > Startup module) (@INC contains: /Applications/freesurfer/mni/lib/.. > /Library/Perl/Updates/5.10.0 /Library/Perl/5.18/darwin-thread-multi- > 2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread- > multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2 > /System/Library/Perl/5.18/darwin-thread-multi-2level > /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin- > thread-multi-2level /System/Library/Perl/Extras/5.18 .) at > /Applications/freesurfer/mni/bin/nu_correct line 37. > BEGIN failed--compilation aborted at > /Applications/freesurfer/mni/bin/nu_correct line 37. > #-------------------------------------------- > #@# MotionCor Sat Dec 26 12:57:51 CET 2015 > ERROR: no run data found in > /Applications/freesurfer/subjects/150622fracal/mri. Make sure to > have a volume called 001.mgz in > /Applications/freesurfer/subjects/150622fracal/mri/orig. > If you have a second run of data call it 002.mgz, etc. > See also: http://surfer.nmr.mgh.harvard. > edu/fswiki/FsTutorial/Conversion > Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue > Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 > > recon-all -s 150622fracal exited with ERRORS at Sat Dec 26 12:57:51 > CET 2015 > > For more details, see the log file > /Applications/freesurfer/subjects/150622fracal/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard. > edu/fswiki/BugReporting > > >>----Messaggio originale---- >>Da: zkauf...@nmr.mgh.harvard.edu >>Data: 26-dic-2015 1.03 >>A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu> >>Cc: <e...@nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] Recon-all error >> >>Hello Emad, >> >> Thank you for reporting this. Its a bug specific to the latest > version >>of OS X (El Capitan). I have committed the fix and it will available >>after the nightly build. You can download via this link: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ >> >>Sorry for the inconvenience and thanks for reporting. >> >>-Zeke >> >> >>> Hi, >>> >>> I ran recon-all on the dicoms of a subject, obtained at Bay 4, and > I >>> received the following error: >>> >>> mris_calc -o lh.area.mid lh.area add lh.area.pial >>> dyld: lazy symbol binding failed: Symbol not found: > ___emutls_get_address >>> Referenced from: >>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib >>> Expected in: /usr/lib/libSystem.B.dylib >>> >>> dyld: Symbol not found: ___emutls_get_address >>> Referenced from: >>> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib >>> Expected in: /usr/lib/libSystem.B.dylib >>> >>> Trace/BPT trap >>> Wed Dec 23 21:59:54 EST 2015 >>> ERROR: vertexvol >>> mris_calc -o lh.area.mid lh.area add lh.area.pial >>> Darwin MGH000844.local 15.2.0 Darwin Kernel Version 15.2.0: Fri Nov > 13 >>> 19:56:56 PST 2015; root:xnu-3248.20.55~2/RELEASE_X86_64 x86_64 >>> >>> recon-all -s 3Lt_002 exited with ERRORS at Wed Dec 23 21:59:54 EST > 2015 >>> >>> For more details, see the log file >>> /Users/Emad/Projects/3LT/subjDir/3Lt_002/scripts/recon-all.log >>> To report a problem, see >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >>> I have attached the log file. Iââ¬â¢d truly appreciate your help. >>> >>> Thank you, and with best wishes for a wonderful holiday season for >>> everyone, >>> Emad >>> >>> >>> Emad Ahmadi, MD >>> ----------------------------------------------- >>> Research Fellow in Radiology >>> Massachusetts General Hospital >>> Harvard Medical School >>> >>> 25 New Chardon Street, Suite 400 >>> Boston, MA 02114 >>> Tel: 617 726 5237 >>> Email: e...@nmr.mgh.harvard.edu >>> >>> _______________________________________________ >>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
