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 -----------------------------------------------------------------------------
I confirmed that the above message does not appear on the linux version of FS5.1.
So, I was wondering if the above situation will cause any problem down the pipeline? I just kept it running for ~18 hours and it seems to be going fine (i.e. at least no problem until the "mris_ca_label" step)
Thank you very much, and I look forward to hearing from you.
Hi,
I am not familiar with the mac build and think Krish can probably give more details. You are missing the libgfortran dynamic library. I don't think it is installed on the mac by default. On the mac we use the veclib framework, not sure why the error shows up and what consequences it has.
You can try registering two images with mri_robust_register (which is not used in recon-all). Recon-all might be influenced because mri_robust_template should show the same problems and that is used for motion correction of several inputs and in the longitudinal stream.
Best, Martin
On May 25, 2011, at 12:30 PM, 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
I confirmed that the above message does not appear on the linux version of FS5.1.
So, I was wondering if the above situation will cause any problem down the pipeline? I just kept it running for ~18 hours and it seems to be going fine (i.e. at least no problem until the "mris_ca_label" step)
Thank you very much, and I look forward to hearing from you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Hyunwoo
Our build system seems to pick up the dynamic gfortran libraries for OSX. We'll post a fixed mri_robust_register ( and similar binaries which depend on that dynamic library) soon.
For a temporary fix:
save ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/libgfortran.2.0.0.dylib to a path.. ( say ~/Downloads )
sudo mkdir -p /usr/local/lib
sudo cp ~/Downloads/libgfortran.2.0.0.dylib /usr/local/lib
cd /usr/local/lib
sudo ln -s libgfortran.2.0.0.dylib libgfortran.2.dylib
You need write permissions for /usr/local/lib . Let us know if it fixes this
-Krish
On May 25, 2011, at 12:30 PM, 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
I confirmed that the above message does not appear on the linux version of FS5.1.
So, I was wondering if the above situation will cause any problem down the pipeline? I just kept it running for ~18 hours and it seems to be going fine (i.e. at least no problem until the "mris_ca_label" step)
Thank you very much, and I look forward to hearing from you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
I confirmed that the above message does not appear on the linux version of FS5.1.
So, I was wondering if the above situation will cause any problem down the pipeline? I just kept it running for ~18 hours and it seems to be going fine (i.e. at least no problem until the "mris_ca_label" step)
Thank you very much, and I look forward to hearing from you.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
And Mac users should wait for this instead of my suggested temporary fix earlier today.
Thanks, -Krish
On May 25, 2011, at 2:57 PM, 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
I confirmed that the above message does not appear on the linux version of FS5.1.
So, I was wondering if the above situation will cause any problem down the pipeline? I just kept it running for ~18 hours and it seems to be going fine (i.e. at least no problem until the "mris_ca_label" step)
Thank you very much, and I look forward to hearing from you.
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
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
I confirmed that the above message does not appear on the linux version of FS5.1.
So, I was wondering if the above situation will cause any problem down the pipeline? I just kept it running for ~18 hours and it seems to be going fine (i.e. at least no problem until the "mris_ca_label" step)
Thank you very much, and I look forward to hearing from you.
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
-
Hyunwoo Lee -
Krish Subramaniam -
Martin Reuter -
Nick Schmansky