Hi Shachar, the patch will not fix this. You’ll probably need to disable SIP - http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ - which prevents access to libraries in /usr. This bug has been fixed in the dev version.

best

Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 13, 2019 at 9:24 AM
To: "ts+ml@rcmd.org" <ts+ml@rcmd.org>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>, Ido Tavor <idotavor@gmail.com>
Subject: Re: [Freesurfer] problem using recon-all

        External Email - Use Caution        

I am not sure that the issue is with the SIP, because the message says this - "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" does not exist in the patches directory, and in fact, it does not exist here - https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/

any ideas where this patch needs to come from?

thanks,

Shachar

On Wed, 13 Feb 2019 at 16:09, Shachar Gal <gal.shachar@gmail.com> wrote:

Hey Tim,

I tried to run the “-E fs_update”, and got this message:

rsync -zbrlv --progress --suffix=.1550066275_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurfer

receiving file list ... 

rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)

0 files to consider

sent 4 bytes  received 9 bytes  8.67 bytes/sec

total size is 0  speedup is 0.00

rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404) [receiver=2.6.9]

Does the indicate I should disable SIP, or is it a different issue?

Thanks,

Shachar