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When I changed the permissions on the directory where FreeSurfer was installed and ran it from there, and all went well. However, when I tried to display the results with Freeview, there was a problem: error while loading shared libraries: libpng12.so.0

This was a more serious error. I saw some mention of this error occurring, but am not sure what to do about it. The answers given don't quite help. Somehow I need to extract a very specific library which I have no idea how to find. I installed all this using Anaconda in a virtual environment. I have several copies of libpng12.so.0 in various conda environments, but not the specific version that seems to be required by Freeview...

On Fri, Dec 20, 2019 at 12:33 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi Rafael,

Is your subject directory stored on an external drive like an SD card? The “Function not implemented” error implies that symlinks are not supported on the filesystem that you’re saving to. Ubuntu 18 definitely supports symlinks and I see that SUBJECTS_DIR points to /media/rafa…. You should process your data on the ubuntu filesystem first, then try copying it onto a card after.

Best,

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rafael Espericueta resperic@ucsc.edu *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, December 18, 2019 at 8:57 PM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Error running "Test your FreeSurfer Installation"

•    External Email - Use Caution        *
  
  

I was trying to run the command: recon-all -s bert -all

It ran for hours, but finally output the following:

writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented Linux hypatia 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s bert exited with ERRORS at Wed Dec 18 16:18:43 PST 2019

1. FreeSurfer version:

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 18.04.3 3) recon-all.log: see attached _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Thanks Kiyotaka,

Unfortunately there's still a problem. Perhaps some pointer isn't set up to point at the proper directory, as I'm getting:

*Command 'freeview' not found*

I ran these commands first: export SUBJECTS_DIR=/usr/local/freesurfer/subjects export FREESURFER_HOME=/usr/local/freesurfer

And have tried starting off (using cd) in each of the above folders.

Do I need to set some other environment variables? It seems that there may be some necessary steps missing from that initial "getting started" tutorial...

On Fri, Dec 20, 2019 at 5:09 PM Kiyotaka Nemoto kiyotaka@nemotos.net wrote:

    External Email - Use Caution

Dear Rafael,

I use Ubuntu 18.04, and installing libpng12 resolved the problem for freeview. Copy and paste the below to your terminal and you will be able to run freeview.

---

curl -O http://security.ubuntu.com/ubuntu/pool/main/libp/libpng /libpng12-0_1.2.54-1ubuntu1.1_amd64.deb sudo apt install -y ./libpng12-0_1.2.54-1ubuntu1.1_amd64.deb

---

Hope this helps,

Kiyotaka

    External Email - Use Caution

...

When I changed the permissions on the directory where FreeSurfer was installed and ran it from there, and all went well. However, when I tried to display the results with Freeview, there was a problem: error while loading shared libraries: libpng12.so.0

This was a more serious error. I saw some mention of this error occurring, but am not sure what to do about it. The answers given don't quite help. Somehow I need to extract a very specific library which I have no idea how to find. I installed all this using Anaconda in a virtual environment. I have several copies of libpng12.so.0 in various conda environments, but not the specific version that seems to be required by Freeview...

On Fri, Dec 20, 2019 at 12:33 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

...

Hi Rafael,

Is your subject directory stored on an external drive like an SD card? The “Function not implemented” error implies that symlinks are not supported on the filesystem that you’re saving to. Ubuntu 18 definitely supports symlinks and I see that SUBJECTS_DIR points to /media/rafa…. You should process your data on the ubuntu filesystem first, then try copying it onto a card after.

Best,

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rafael Espericueta resperic@ucsc.edu *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, December 18, 2019 at 8:57 PM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Error running "Test your FreeSurfer Installation"

•    External Email - Use Caution        *
  
  

I was trying to run the command: recon-all -s bert -all

It ran for hours, but finally output the following:

writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented Linux hypatia 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s bert exited with ERRORS at Wed Dec 18 16:18:43 PST 2019

1. FreeSurfer version:

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 18.04.3 3) recon-all.log: see attached _______________________________________________ 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

-- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyotaka@nemotos.net _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Aha, that did it! There was one small additional snag - my "bert" directory was under "subjects", but was being looked for in the freesurfer folder. So I moved the "bert" folder to where freeview was looking for it, and all is well.

Thanks everyone for your help! :-)

On Sat, Dec 21, 2019 at 10:48 AM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi Rafael, you must source the FS environment before running things:

source $FREESURFER_HOME/SetUpFreeSurfer.sh

Which ‘getting started’ tutorial are you looking at? This step is documented in the ‘Setup & Configuration’ section.

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rafael Espericueta resperic@ucsc.edu *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Saturday, December 21, 2019 at 1:10 PM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Error running "Test your FreeSurfer Installation"

•    External Email - Use Caution        *
  
  

Thanks Kiyotaka,

Unfortunately there's still a problem. Perhaps some pointer isn't set up to point at the proper directory, as I'm getting:

*Command 'freeview' not found*

I ran these commands first:

export SUBJECTS_DIR=/usr/local/freesurfer/subjects export FREESURFER_HOME=/usr/local/freesurfer

And have tried starting off (using cd) in each of the above folders.

Do I need to set some other environment variables? It seems that there may be some necessary steps missing from that initial "getting started" tutorial...

On Fri, Dec 20, 2019 at 5:09 PM Kiyotaka Nemoto kiyotaka@nemotos.net wrote:

•    External Email - Use Caution        *
  
  

Dear Rafael,

I use Ubuntu 18.04, and installing libpng12 resolved the problem for freeview.

Copy and paste the below to your terminal and you will be able to run freeview.

---

curl -O http://security.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1u...

sudo apt install -y ./libpng12-0_1.2.54-1ubuntu1.1_amd64.deb

---

Hope this helps,

Kiyotaka

•    External Email - Use Caution        *
  
  

When I changed the permissions on the directory where FreeSurfer was installed and ran it from there, and all went well. However, when I tried to display the results with Freeview, there was a problem: error while loading shared libraries: libpng12.so.0

This was a more serious error. I saw some mention of this error occurring, but am not sure what to do about it. The answers given don't quite help. Somehow I need to extract a very specific library which I have no idea how to find. I installed all this using Anaconda in a virtual environment. I have several copies of libpng12.so.0 in various conda environments, but not the specific version that seems to be required by Freeview...

On Fri, Dec 20, 2019 at 12:33 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi Rafael,

Is your subject directory stored on an external drive like an SD card? The “Function not implemented” error implies that symlinks are not supported on the filesystem that you’re saving to. Ubuntu 18 definitely supports symlinks and I see that SUBJECTS_DIR points to /media/rafa…. You should process your data on the ubuntu filesystem first, then try copying it onto a card after.

Best,

Andrew

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rafael Espericueta resperic@ucsc.edu *Reply-To: *FS Help freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, December 18, 2019 at 8:57 PM *To: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Error running "Test your FreeSurfer Installation"

•    External Email - Use Caution        *
  
  

I was trying to run the command: recon-all -s bert -all

It ran for hours, but finally output the following:

writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Function not implemented Linux hypatia 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s bert exited with ERRORS at Wed Dec 18 16:18:43 PST 2019

1. FreeSurfer version:

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu 18.04.3 3) recon-all.log: see attached

---

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

--

Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyotaka@nemotos.net

---

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