Dear Andrew, 


thank you very much! Yes, you were right! Now it works fine. 


best regards 


Dusan



From: Hoopes, Andrew <AHOOPES@mgh.harvard.edu>
Sent: Tuesday, February 13, 2018 12:23 PM
To: Freesurfer support list; Dusan Hirjak
Subject: Re: [Freesurfer] Problems running LGI
 
Hi Dusan, I just remembered that this is probably due to SIP being enabled on your mac, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: MailScanner has detected a possible fraud attempt from "nam04.safelinks.protection.outlook.com" claiming to be http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

best,
Andrew


On February 12, 2018 at 10:28:09 AM, Hoopes, Andrew (ahoopes@mgh.harvard.edu) wrote:

Hi Dusan,

I’ll take a look at this and get back to you soon. I think this issue is related to the matlab version.

best
Andrew


On February 10, 2018 at 4:27:11 PM, Dusan Hirjak (dusanhirjak@hotmail.com) wrote:

Dear Freesurfer Experts, 


I am currently trying to run LGI. I have the 2017b Matlab version, Mac OS Sierra and I already set up the freesurfer PATH in Matlab. However, I am getting the following error after starting recon all -s localGI :


Dusans-MacBook-Pro:NSS_Analysis_01 dusan$ recon-all -s SP002 -localGI

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/NSS_Analysis_01

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r--  1 dusan  wheel  508655 Jul 29  2017 /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/scripts/recon-all.log

Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64

/Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf

#--------------------------------------------

#@# Local Gyrification Index lh Sat Feb 10 21:59:13 CET 2018

\n mris_compute_lgi --i lh.pial \n

=================

rm -Rf /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial

=================

=================

mkdir -p /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial

=================

=================

mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz

=================

reading surface from lh.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


Abort

ERROR: mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed!

Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64



Any help would be greatly appreciated! Many thanks, Dusan

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