Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

mri_surfcluster on group
by stdp82＠virgilio.it 29 Dec '15

29 Dec '15

Hi list,I'd like to perform mri_surfcluster on a group to eliminate cluster < 5 voxels from sig.nii.gz after FDR correction.I'm running mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum summaryfile --ocn ocnid but --subject ... must be included. How should do I do? My analysis should be run on group results, not on a subject. Thanks, Stefano

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How can I use mri_vol2surf to map the white matter volume cortical surface in order to generate a white matter map that is similar to the gray matter volume map produced by mris_preproc?
by Knut J Bjuland 28 Dec '15

28 Dec '15

DearFreeSurferexperts, HowcanIusemri_vol2surftomapthewhitemattervolumecorticalsurfaceinordertogenerateawhitemattermapthatissimilartothegraymattervolumemapproducedbymris_preproc? ShouldIusebinarymaskcreatedinMatlabtoremovelabelsthatarenotwhitematter? Best regards KnutJørgenBjuland NTNU

1 0

visualization of a "spherical" cut
by Krieger, Donald N. 28 Dec '15

28 Dec '15

Dear List, I have a visualization problem which is not directly relevant to freesurfer but which may be easily solvable with the freesurfer tools. I have also posted this question to the ImageJ discussion list. I would like to visualize "spherical" cuts through an MR. An axial cut is the intersection of the image volume with a plane normal to a line running superior to inferior through the volume. A spherical cut is the intersection of a sphere with specified origin through the volume. Hence the visual would be a disc with radius that of the sphere and center at the origin. There would be two such discs, one for the front and one for the back. What do you think? Is there an easy way? Any thought and/or suggestions would be welcome. Thanks - Don

1 0

missing 3volreg.afni
by Thục Trinh 27 Dec '15

27 Dec '15

Hi FS experts, I'm working on my fMRI data using FSFAST v.6 tool. But the first step of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI command 3dvolreg.afni ". * I found a thread that had the same error with mine (in FS v.5.3) : http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html But the link to download 3dvolreg.afni doesn't work. Is this the same 3dvolreg.afni for v.5.3 and v.6? Thanks, Trinh

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PhD position: MRI markers of neuroinflammation in treatment pharmacoresistant epilepsy
by Barbara Kreilkamp 27 Dec '15

27 Dec '15

Dear Freesurfers, A PhD studentship „Identifying non-invasive imaging markers of neuroinflammation in treatment pharmacoresistant epilepsy“ is available in the Epilepsy Research Group (ERG) at the University of Liverpool, UK and is supervised by Dr Simon Keller and Prof Tony Marson. Please find all details about this position via this link: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=70289&LID=3417 *Deadline:* Friday, January 22, 2016 - apply ASAP! Best wishes and a Happy New Year! Barbara Kreilkamp PhD researcher University of Liverpool

1 0

Integrating planes into a single volume?
by John Benfield 27 Dec '15

27 Dec '15

Is there any way to integrate the information from axial, coronal and sagittal views into a single volume? I'm looking for ways to build a more accurate/comprehensive 3d model and I'm not having any luck finding workflows or tools that allow any sort of cross-plane refinement/interpolation. Any suggestions?

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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 >

2 1

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. > >

2 1

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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