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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-Linu... - 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-... $ curl -O http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-... - 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 <marfneuro@GMAIL.COM> 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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 http://cachedarray.cc/ crash bug.
Joe
On May 31, 2019, at 18:39, fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionHello 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-Linu... 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-... 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-...
- 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 marfneuro@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 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
--------------------------------------------------------------------------------
Joseph Dien, PhD Senior Research Scientist Department of Human Development and Quantitative Methodology University of Maryland, College Park http://joedien.com
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
Joseph Dien