Re: [Freesurfer] FreeSurfer LocalGI error
Thank you very much, Dear Andrew! for your expert advise. I really appreciated. Its worked. Best Regards Manoj On Tue, Jan 16, 2018 at 10:39 PM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Hi Manoj, > > This probably has to do with SIP being enabled, which blocks libraries > stored in /usr. I would suggest disabling SIP and rerunning to see if > that fixes things: > http://osxdaily.com/2015/10/05/disable-rootless-system- > integrity-protection-mac-os-x/ > > best, > Andrew > > > On Jan 16, 2018, at 2:59 AM, Manoj Kumar <verman...@gmail.com> wrote: > > Hello Dear FreeSurfer Experts, > > I am trying to run "recon-all -s subject -localGI" command on my Mac bash > terminal. I am getting following error. > > I am using using Freesurfer V 6.0 and running on MacOS High Sierra > (version 10.13) > > I also run the istallation update :"sudo -E fs_update" as per suggestion > on the release note but still getting same error. > > Any help to resolve this issue would be greatly appreciated. > Thank you so much for all your help and support. > > Best regards > Manoj > > *** > Manojs-iMac:cases manojkumar$ export SUBJECTS_DIR=/Users/ > manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf > Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR > Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial > = > rm -Rf /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/ > surf/tmp-mris_compute_lgi-lh.pial > = > = > mkdir -p /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/ > surf/tmp-mris_compute_lgi-lh.pial > = > = > mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_ > process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh. > pial/lh.pial.filled.mgz > = > 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 > > Abort > ERROR: mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_ > process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz > failed! > Manojs-iMac:surf manojkumar$ > ___ > 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] FreeSurfer LocalGI error
Hello Dear FreeSurfer Experts, I am trying to run "recon-all -s subject -localGI" command on my Mac bash terminal. I am getting following error. I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version 10.13) I also run the istallation update :"sudo -E fs_update" as per suggestion on the release note but still getting same error. Any help to resolve this issue would be greatly appreciated. Thank you so much for all your help and support. Best regards Manoj *** Manojs-iMac:cases manojkumar$ export SUBJECTS_DIR=/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial = rm -Rf /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial = = mkdir -p /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial = = mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz = 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 Abort ERROR: mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Manojs-iMac:surf manojkumar$ ___ 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.
Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Hello Dear Sir/Madam, Please provide your expert suggestions to resolve the above-mentioned error. Thank you very much, Best regards Manoj On Sat, Nov 18, 2017 at 11:05 AM, Manoj Kumar <verman...@gmail.com> wrote: > Hello Dear Sir/Madam, > > I am fairly new to the freesurfer and am getting an error "ERROR: > mpr2mni305 failed, see transforms/talairach_avi.log" > > When I run the "recon-all -all -subjid Anj commond. > > I looked for this error message on https://mail.nmr.mgh. > harvard.edu/pipermail//freesurfer/2014-August/039761.html > But could not resolve this issue by myself. > I am here also attaching the complete error log and recon-all-error file > for your find attention. > > Please kindly provide your expert suggestions to resolve this issue. > Please let me know if you need any additional information for further > diagnosis of the error. > > Thank you very much for all your help and support. > > Best > > ___ 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.
