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-boun...@nmr.mgh.harvard.edu> on behalf of Shachar Gal
<gal.shac...@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 13, 2019 at 9:24 AM
To: "ts...@rcmd.org" <ts...@rcmd.org>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>, Ido Tavor <idota...@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.shac...@gmail.com<mailto:gal.shac...@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
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