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-... - 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.commailto: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