Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

R: Re: R: Re: R: Re: Recon-all error
by stdp82＠virgilio.it 27 Dec '15

27 Dec '15

Hi Zeke, please look this error. Thanks Stefano recon-all -all -s 150706samspe/T1_STRUCT.nii.gz -i $SUBJECTS_DIR/150706samspe/T1_STRUCT.nii.gz -hippocampal-subfields-T1 Subject Stamp: freesurfer-Darwin-OSX-dev-20151214 Current Stamp: freesurfer-Darwin-OSX-dev-20151214 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer 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 /Applications/freesurfer/subjects/T1_STRUCT.nii.gz \n mri_convert /Applications/freesurfer/subjects/150706samspe/T1_STRUCT.nii.gz /Applications/freesurfer/subjects/T1_STRUCT.nii.gz/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/150706samspe/T1_STRUCT. nii.gz /Applications/freesurfer/subjects/T1_STRUCT.nii.gz/mri/orig/001. mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /Applications/freesurfer/subjects/150706samspe/T1_STRUCT. nii.gz... 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 T1_STRUCT.nii.gz exited with ERRORS at Sun Dec 27 14:17: 52 CET 2015 For more details, see the log file /Applications/freesurfer/subjects/T1_STRUCT.nii.gz/scripts/recon-all. log To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting >----Messaggio originale---- >Da: zkaufman(a)nmr.mgh.harvard.edu >Data: 27-dic-2015 3.42 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh. harvard.edu> >Cc: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: Recon-all error > >>From the recon-all wiki page under "specify input": > > https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Specifyinput > >In this case you would use the -i flag to point to dicom file or nifti. >For example: > > recon-all -all -s 150622fracal -i </path/to/input_volume> >-hippocampal-subfields-T1 > >-Zeke > > >> Hi Zeke, >> I'm sorry but I do not understand how run the correct command line. >> Where I should use --i? >> Thanks >> >> >> Stefano >> >> >>>----Messaggio originale---- >>>Da: zkaufman(a)nmr.mgh.harvard.edu >>>Data: 26-dic-2015 21.50 >>>A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer@nmr. mgh. >> harvard.edu> >>>Cc: <freesurfer(a)nmr.mgh.harvard.edu> >>>Ogg: Re: [Freesurfer] R: Re: Recon-all error >>> >>> >>>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: zkaufman(a)nmr.mgh.harvard.edu >>>>>Data: 26-dic-2015 1.03 >>>>>A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> >>>>>Cc: <emad(a)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. IÃƒÂ¢Ã¢â€šÂ¬Ã¢â€žÂ¢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: emad(a)nmr.mgh.harvard.edu >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>>_______________________________________________ >>>>>Freesurfer mailing list >>>>>Freesurfer(a)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(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>>_______________________________________________ >>>Freesurfer mailing list >>>Freesurfer(a)nmr.mgh.harvard.edu >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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R: Re: R: Re: Recon-all error
by stdp82＠virgilio.it 26 Dec '15

26 Dec '15

Hi Zeke, I'm sorry but I do not understand how run the correct command line. Where I should use --i? Thanks Stefano >----Messaggio originale---- >Da: zkaufman(a)nmr.mgh.harvard.edu >Data: 26-dic-2015 21.50 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh. harvard.edu> >Cc: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: Recon-all error > > >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: zkaufman(a)nmr.mgh.harvard.edu >>>Data: 26-dic-2015 1.03 >>>A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> >>>Cc: <emad(a)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. IÃ¢â‚¬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: emad(a)nmr.mgh.harvard.edu >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>_______________________________________________ >>>Freesurfer mailing list >>>Freesurfer(a)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(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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R: Re: Recon-all error
by stdp82＠virgilio.it 26 Dec '15

26 Dec '15

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: zkaufman(a)nmr.mgh.harvard.edu >Data: 26-dic-2015 1.03 >A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> >Cc: <emad(a)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. Iâ€™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: emad(a)nmr.mgh.harvard.edu >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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. > >

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Recon-all error
by Emad Ahmadi 25 Dec '15

25 Dec '15

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. I’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: emad(a)nmr.mgh.harvard.edu

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fast-selxavg3 error: input to SVD must not contain NaN or Inf
by zhang mingxia 25 Dec '15

25 Dec '15

Dear experts, I run selxavg3-sess for retinotopy analysis and get the error below: Input to SVD must not contain NaN or Inf Error in cond (line 39) s = svd(A) Error in fast_selxavg3(line 254) XCond = cond(XtX) I am also sending the log file and Xtmp.mat. Hope to get the help. Thank you very much in advance. Mingxia Zhang

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Re: [Freesurfer] recon all erro
by Hassan bakhshi 24 Dec '15

24 Dec '15

Hi emad, I think if you change format type of images to nifti it will work as allright. I had a problem like this and it worked for me... On Dec 24, 2015 8:30 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Recon-all error (Emad Ahmadi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 Dec 2015 09:50:52 -0500 > From: Emad Ahmadi <emad(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Recon-all error > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <B3495F09-E1E9-4057-B839-C407B2182364(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > 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. I?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: emad(a)nmr.mgh.harvard.edu > >

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Re: [Freesurfer] recon-all issue
by Schell, Susanne 23 Dec '15

23 Dec '15

Dear colleagues, We are recently using the freesurfer recon-all command recon-all -s XXXX -I XXXX.nii.gz recon-all -s XXXX -all where XXXX stands for the subject ID. I have been trying to execute this command with the different input files: 1) original dicom-files 2) nii-file where the field of view was cut, apart from that the same file as in 3) 3) nii.gz-file, was computed by mri_convert with the files from 1) We guessed results should be the same, but unfortunately, the segmentation looks slightly different in all three cases. Maybe you can help us by trying to find out why the output files are different? Thanks very much in advance! Best regards, Susanne ______________________________________ Susanne Schell, Dipl.-Psych. Sektion Störungen der Persönlichkeitsentwicklung Klinik für Kinder- und Jugendpsychiatrie Universitätsklinikum Heidelberg Tel: (+49) - (0)6221-56 35135 e-mail: susanne.schell(a)med.uni-heidelberg.de<mailto:susanne.schell@med.uni-heidelberg.de>

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recon-all error
by abdulkawi alareefi alareefi 22 Dec '15

22 Dec '15

Hi Freesurfers, I am currently learning how to use freesurfer to process the brain image and I acknowledge your great job. I contacting you regarding that I got an error after using recon-all command. By the way i am sill beginner in both linux and freesurer. Here is the log of the error abdol@abdol-pc:~$ recon-all -s mine -all Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/abdol/Desktop/freesurfer/subjects Actual FREESURFER_HOME /home/abdol/Desktop/freesurfer -rw-rw-r-- 1 abdol abdol 100038 12月 22 10:59 /home/abdol/Desktop/freesurfer/subjects/mine/scripts/recon-all.log Linux abdol-pc 3.13.0-73-generic #116-Ubuntu SMP Fri Dec 4 15:31:30 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor 2015年 12月 23日星期三 11:01:18 CST ERROR: no run data found in /home/abdol/Desktop/freesurfer/subjects/mine/mri. Make sure to have a volume called 001.mgz in /home/abdol/Desktop/freesurfer/subjects/mine/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 Linux abdol-pc 3.13.0-73-generic #116-Ubuntu SMP Fri Dec 4 15:31:30 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mine exited with ERRORS at 2015年 12月 23日星期三 11:01:18 CST For more details, see the log file /home/abdol/Desktop/freesurfer/subjects/mine/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Regards Abdulqawi Alarefi

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Re: [Freesurfer] Recon-all: Pial surface error in cingulate region
by Jaiashre Sridhar 22 Dec '15

22 Dec '15

Dr. Fischl, Since it is a longitudinal study, we have to stick to using 5.1 version. Thanks, Jaiashre.

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Re: [Freesurfer] Recon-all: Pial surface error in cingulate region
by Jaiashre Sridhar 22 Dec '15

22 Dec '15

Dr. Fischl, I am using FS version 5.1.0 Thanks, Jaiashre.

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Freesurfer December 2015