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I am trying to install FreeSurfer: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz It's not available for Windows, so I have installed ubuntu-16.10-desktop-i386.iso on VirtualBox.

I am following these steps to install FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

I am able to successfully execute following commands:

tar -C /home/gyan -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
export FREESURFER_HOME=/home/gyan/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
sudo apt install tcsh
tcsh
setenv FREESURFER_HOME /home/gyan/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
exit
cp $FREESURFER_HOME/subjects/sample-001.mgz .

But, I am getting this error, when I run mri_convert sample-001.mgz sample-001.nii.gz:

mri_convert.bin: cannot execute binary file: Exec format error

I am totally new to Linux, please help!

I am using Windows 10 (64-bit), Intel i7-4710HQ.

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    Since you installed the ubuntu-16.10-desktop-i386.iso in your VM, you not be able to run 64-bit (x86_64) software in it. Either you will need to find a 32-bit version of 'freesurfer' or will need to install a 64-bit version of Ubuntu
    – steeldriver
    Mar 22, 2017 at 17:44

1 Answer 1

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Check the directory location where you are when you are executing that last line, because I had the same problem but I'm not sure why it worked:

cd home/$USER/Downloads/freesurfer/subjects

[now you are in that freesurfer folder]

mri_convert sample-001.mgz
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