I've encountered the same problem described below despite downloading the new version posted on 26th May.
I downloaded freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg today from http://www.freesurfer.net/fswiki/Download
I'm running Mac OS X version 10.6.7 (Intel)
On attempting to test the installation as described in the instructions with tkmedit bert orig.mgz I get the message
dyld: Library not loaded: /usr/pubsw/packages/tcltktixblt/current/lib/libtk8.4.dylib Referenced from: /Applications/IRIS/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap
Is this the same library dependency issue, i.e. it's not fully fixed in the latest download at least not for my OS? I couldn't find any more recent posts but am new to the list, so apologies if I have.
Thanks Mike Nick Schmansky Thu, 26 May 2011 05:59:24 -0700 Hyunwoo (and Mac users), A new build of v5.1 for the Mac (Leopard and Snow Leopard) has been posted. If you downloaded the one posted on May 24th, you will need to get this new one, as the one from May 24th depended on libgfortran, which is not installed natively. Sorry for any inconvenience. N. On Wed, 2011-05-25 at 14:57 -0400, Nick Schmansky wrote: > Hyunwoo (and Mac users), > > We're going to have to post a new build of v5.1 later today which fixes > this problem. In general, our goal is to have a Mac build that doesnt > require special libraries, like libgfortran, but both our build and test > machines had that lib for other reasons, so it slipped through the > cracks during testing. > > I'll post to the list when its ready. It will be identical in usage to > the current Mac 5.1, just without the libgfortran dynamic lib > dependency. > > Nick > > > On Wed, 2011-05-25 at 16:30 +0000, Hyunwoo Lee wrote: > > Dear FreeSurfer > > > > Hello, I am currently trying the following freesurfer version: > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg > > and I noticed the following. > > During the first step ( recon-all -i invol1 -i invol2 -subjid > > your_subject_name ), the console displays the following messages: > > ------------------------------------------------------------------------------- > > Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > INFO: SUBJECTS_DIR is ******* > > Actual FREESURFER_HOME /Applications/freesurfer > > Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 > > PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 > > dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib > > Referenced from: /Applications/freesurfer/bin/mri_robust_register > > Reason: image not found > > Trace/BPT trap > > dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib > > Referenced from: /Applications/freesurfer/bin/mri_robust_register > > Reason: image not found > > Trace/BPT trap
Hi Mike
Sorry. Our OSX builds seem to pick up the dynamic libraries for a few binaries during the build process. These things escape our internal testing because the binaries work here.
We'll post a new build which takes care of this issue. This can be just installed over the existing 5.1 version because the only significant fix made is the issue you pointed out.
-Krish
On Jun 7, 2011, at 11:05 AM, Michael O'Sullivan wrote:
I've encountered the same problem described below despite downloading the new version posted on 26th May.
I downloaded freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg today from http://www.freesurfer.net/fswiki/Download
I'm running Mac OS X version 10.6.7 (Intel)
On attempting to test the installation as described in the instructions with tkmedit bert orig.mgz I get the message
dyld: Library not loaded: /usr/pubsw/packages/tcltktixblt/current/ lib/libtk8.4.dylib Referenced from: /Applications/IRIS/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap
Is this the same library dependency issue, i.e. it's not fully fixed in the latest download at least not for my OS? I couldn't find any more recent posts but am new to the list, so apologies if I have.
Thanks Mike
Nick Schmansky Thu, 26 May 2011 05:59:24 -0700
Hyunwoo (and Mac users),
A new build of v5.1 for the Mac (Leopard and Snow Leopard) has been posted. If you downloaded the one posted on May 24th, you will need to get this new one, as the one from May 24th depended on libgfortran, which is not installed natively. Sorry for any inconvenience.
N.
On Wed, 2011-05-25 at 14:57 -0400, Nick Schmansky wrote:
Hyunwoo (and Mac users),
We're going to have to post a new build of v5.1 later today which
fixes
this problem. In general, our goal is to have a Mac build that
doesnt
require special libraries, like libgfortran, but both our build
and test
machines had that lib for other reasons, so it slipped through the cracks during testing.
I'll post to the list when its ready. It will be identical in
usage to
the current Mac 5.1, just without the libgfortran dynamic lib dependency.
Nick
On Wed, 2011-05-25 at 16:30 +0000, Hyunwoo Lee wrote:
Dear FreeSurfer
Hello, I am currently trying the following freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg
and I noticed the following. During the first step ( recon-all -i invol1 -i invol2 -subjid your_subject_name ), the console displays the following messages:
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is ******* Actual FREESURFER_HOME /Applications/freesurfer Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29
15:17:16
PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Applications/freesurfer/bin/mri_robust_register Reason: image not found Trace/BPT trap dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Applications/freesurfer/bin/mri_robust_register Reason: image not found Trace/BPT trap
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mike
Did you overwrite the existing FS distribution with the 5.1 version? We do copy the shared libraries tkmedit and others need.
Can you do "ls -al" of the following 4 files and give us the
- file dates of tkmedit and tkmedit.bin in bin dir - file dates of tkmedit and tkmedit.bin in tktools dir
The installation needs to copy these files to both the locations and we think that it didn't do it somehow.
-Krish
On Tue, Jun 07, 2011 at 01:32:56PM -0400, Krish Subramaniam wrote:
Hi Mike
Sorry. Our OSX builds seem to pick up the dynamic libraries for a few binaries during the build process. These things escape our internal testing because the binaries work here.
We'll post a new build which takes care of this issue. This can be just installed over the existing 5.1 version because the only significant fix made is the issue you pointed out.
-Krish
On Jun 7, 2011, at 11:05 AM, Michael O'Sullivan wrote:
I've encountered the same problem described below despite downloading the new version posted on 26th May.
I downloaded freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg today from http://www.freesurfer.net/fswiki/Download
I'm running Mac OS X version 10.6.7 (Intel)
On attempting to test the installation as described in the instructions with tkmedit bert orig.mgz I get the message
dyld: Library not loaded: /usr/pubsw/packages/tcltktixblt/current/ lib/libtk8.4.dylib Referenced from: /Applications/IRIS/freesurfer/tktools/tkmedit.bin Reason: image not found Trace/BPT trap
Is this the same library dependency issue, i.e. it's not fully fixed in the latest download at least not for my OS? I couldn't find any more recent posts but am new to the list, so apologies if I have.
Thanks Mike
Nick Schmansky Thu, 26 May 2011 05:59:24 -0700
Hyunwoo (and Mac users),
A new build of v5.1 for the Mac (Leopard and Snow Leopard) has been posted. If you downloaded the one posted on May 24th, you will need to get this new one, as the one from May 24th depended on libgfortran, which is not installed natively. Sorry for any inconvenience.
N.
On Wed, 2011-05-25 at 14:57 -0400, Nick Schmansky wrote:
Hyunwoo (and Mac users),
We're going to have to post a new build of v5.1 later today which
fixes
this problem. In general, our goal is to have a Mac build that
doesnt
require special libraries, like libgfortran, but both our build
and test
machines had that lib for other reasons, so it slipped through the cracks during testing.
I'll post to the list when its ready. It will be identical in
usage to
the current Mac 5.1, just without the libgfortran dynamic lib dependency.
Nick
On Wed, 2011-05-25 at 16:30 +0000, Hyunwoo Lee wrote:
Dear FreeSurfer
Hello, I am currently trying the following freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0.dmg
and I noticed the following. During the first step ( recon-all -i invol1 -i invol2 -subjid your_subject_name ), the console displays the following messages:
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is ******* Actual FREESURFER_HOME /Applications/freesurfer Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29
15:17:16
PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Applications/freesurfer/bin/mri_robust_register Reason: image not found Trace/BPT trap dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Applications/freesurfer/bin/mri_robust_register Reason: image not found Trace/BPT trap
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Krish Subramaniam -
Michael O'Sullivan