Hi Jay, Try calling "source $FREESURFER_HOME/SetUpFreeSurfer.csh” (without the quotes) at the beginning of @SUMA_Make_Spec_FS (it’s a script that should be wherever AFNI is installed, like $HOME/abin).
Cheers, Ruy > On Mar 26, 2018, at 12:54 PM, Hoopes, Andrew <[email protected]> wrote: > > Hi Jay, as a temporary fix for 6.0, I would suggest disabling SIP and > rerunning: > http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ > > <http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/> > > best > Andrew > > From: <[email protected]> on behalf of Jay Edelman > <[email protected]> > Reply-To: FS Help <[email protected]> > Date: Thursday, March 22, 2018 at 10:02 PM > To: FS Help <[email protected]> > Subject: [Freesurfer] Problem running mri_convert > > Dear Freesurfers, > > I am running the program "mri_convert" within the AFNI script, > @SUMA_Make_Spec_FS, and am receiving the error below. I just installed > freesurfer from your website and am running this on a Mac running Yosemite. > I've looked at the online forums and see this addressed in other contexts, > but unfortunately I can't find any fix. > > Thanks So Much! > Jay Edelman > Dept. of Biology, The City College of New York > > mri_convert.bin -ot nii mri/wm.seg.mgz > /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from mri/wm.seg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0, -1) > k_ras = (0, 1, 0) > writing to /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii... > -- running 'mris_convert lh.smoothwm lh.smoothwm.asc' > Trace/BPT trap > 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 > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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 [email protected] 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.
