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: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-...https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fosxdaily.com%2F2015%2F10%2F05%2Fdisable-rootless-system-integrity-protection-mac-os-x%2F&data=02%7C01%7C%7Cdb43e88111a84d4e7b9008d5731fb1a3%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636541502307376874&sdata=Lug8lGkQVb7mO6CpA5%2BQmATfO0lf8IuoTfqvyG5LNdw%3D&reserved=0

best, Andrew

On February 12, 2018 at 10:28:09 AM, Hoopes, Andrew (ahoopes@mgh.harvard.edumailto: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.commailto: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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