Re: [Freesurfer] Freesurfer V6 installation: ubuntu virtual machine

2019-06-03 Thread Joseph Dien 
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I have successfully run freesurfer 6.0 recon-all under Ubuntu in the OS X 
Parallels VM, as a workaround for the OS X recon-all CachedArray.cc 
 crash bug.

Joe

> On May 31, 2019, at 18:39, fsbuild  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello Steve,
> 
> We have run the freesurfer 6.0.0 release on Ubuntu 16 and 18 which should 
> also work in a VM.
> 
> You may have to install some packages in order to run freesurfer, especially 
> for the freeview program which uses various graphics packages, etc.  After 
> downloading the freesurfer 6.0.0 binaries from,
> 
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
>  
> 
> 
> - I would first try to run the freeview binary as that is a good test to help 
> determine what packages may be missing.
> 
> I needed to both build and run freesurfer on Ubuntu, so I will list below the 
> packages I installed for both purposes.  You should not need for example the 
> gcc compiler packages just to run the 6.0.0 release binaries, but I have not 
> tried to identify a set of packages to only run the binaries.
> 
> You will likely also need sudo privileges to install packages.
> 
> - R.
> 
>  $ sudo apt-get install build-essential
>  $ sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev
>  $ sudo apt-get install libblas-dev liblapack-dev
>  $ sudo apt-get install ocl-icd-opencl-dev
>  $ sudo apt-get install libxmu-dev libxi-dev
>  $ sudo apt-get install libopencv-dev 
> 
>  Ubuntu 16:  $ sudo apt-get install gcc-4.9 g++-4.9 gfortran-4.9
>  Ubuntu 18:  $ sudo apt-get install gcc-4.8 g++-4.8 gfortran-4.8
> 
>  $ sudo apt-get install xorg xorg-dev libx11-dev
>  $ sudo apt-get install tcl tcl-dev tk tk-dev
>  $ sudo apt-get install qt5-default qtcreator
>  $ sudo apt-get install libqt5x11extras5-dev
>  $ sudo apt-get install git-annex 
>  $ sudo apt-get install python3-dev
> 
> … you will need a libpng, which I got from the archives,
> 
> 
> http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
>  
> 
> 
> $ curl -O  
> http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
> 
>- then install the gdebi tool, 
> 
> $ sudo  apt install gdebi
> 
> - change directories to where you downloaded the libpng12 package, and 
> use gdebi to install it,
> 
> $ sudo  gdebi  libpng12-0_1.2.54-1ubuntu1_amd64.deb
> 
> 
> 
>> On May 31, 2019, at 02:57, Steve Petersen  wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Dear Freesurfer experts, 
>> 
>> 
>> Just a simple question, is possible to install the Freesurfer (Version 6) in 
>> a virtual machine of ubuntu?
>> 
>> Thanks in advance,
>> 
>> 
>> Best regards,
>> 
>> Steve
>> ___
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> 
> ___
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Joseph Dien, PhD
Senior Research Scientist
Department of Human Development and Quantitative Methodology
University of Maryland, College Park
http://joedien.com

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Re: [Freesurfer] Freesurfer V6 installation: ubuntu virtual machine

2019-05-31 Thread fsbuild 
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Hello Steve,
We have run the freesurfer 6.0.0 release on Ubuntu 16 and 18 which should also 
work in a VM.

You may have to install some packages in order to run freesurfer, especially 
for the freeview program which uses various graphics packages, etc. After 
downloading the freesurfer 6.0.0 binaries from,
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
- I would first try to run the freeview binary as that is a good test to help 
determine what packages may be missing.
I needed to both build and run freesurfer on Ubuntu, so I will list below the 
packages I installed for both purposes. You should not need for example 
the gcc compiler packages just to run the 6.0.0 release binaries, but I have 
not tried to identify a set of packages to only run the binaries.
You will likely also need sudo privileges to install packages.
- R.
  $ sudo apt-get install build-essential  $ 
sudo apt-get install libgl1-mesa-dev freeglut3-dev mesa-common-dev  
$ sudo apt-get install libblas-dev liblapack-dev  $ 
sudo apt-get install ocl-icd-opencl-dev  $ sudo apt-get 
install libxmu-dev libxi-dev  $ sudo apt-get install 
libopencv-dev  Ubuntu 16: $ sudo apt-get install 
gcc-4.9 g++-4.9 gfortran-4.9  Ubuntu 18: $ sudo apt-get 
install gcc-4.8 g++-4.8 gfortran-4.8  $ sudo apt-get install 
xorg xorg-dev libx11-dev  $ sudo apt-get install tcl tcl-dev 
tk tk-dev  $ sudo apt-get install qt5-default qtcreator 
 $ sudo apt-get install libqt5x11extras5-dev  $ 
sudo apt-get install git-annex  $ sudo apt-get install 
python3-dev
 … you will need a libpng, which I got from the archives,
 
http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
  $curl -O 
http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64..deb
 - then install the gdebi tool,
  $ sudo apt install gdebi
  - change directories to where you downloaded the libpng12 
package, and use gdebi to install it,
  $ sudo gdebi libpng12-0_1.2.54-1ubuntu1_amd64.deb


On May 31, 2019, at 02:57, Steve Petersen marfne...@gmail.com 
wrote:External Email - Use 
CautionDear Freesurfer 
experts,Just a simple question, is possible to install the Freesurfer 
(Version 6) in a virtual machine of ubuntu?Thanks in advance,Best 
regards,Steve___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Freesurfer V6 installation: ubuntu virtual machine

2019-05-31 Thread Steve Petersen 
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Dear Freesurfer experts,


Just a simple question, is possible to install the Freesurfer (Version 6)
in a virtual machine of ubuntu?

Thanks in advance,


Best regards,

Steve
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