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Try $ apt purge fsl-complete fsl-5.0-complete fsl-core fsl-5.0-core make shure all fsl related packages are removed $ dpkg -l | grep fsl If there are any fsl packages left, purge them Reinstall with $ apt install fsl-5.0-complete fsl-5.0-core ________________________________ Von: FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag von Ali Golestani <[log in to unmask]> Gesendet: Freitag, 9. September 2016 16:21 An: [log in to unmask] Betreff: Re: [FSL] AW: [FSL] AW: [FSL] Problem installing FSL on ubuntu 16.04 It seems that there is an incomplete version of FSL hidden somewhere on my computer. Is there a way to remove FSL and everything related to it and install it again? On Thu, Sep 8, 2016 at 9:48 AM, Ali Golestani <[log in to unmask]<mailto:[log in to unmask]>> wrote: FSLDIR is /usr/share/fsl/5.0. The problem is there is no such a folder on my computer Before Sourcing the fsl configuration fslview whoud run, but for fsl I got the message: "fsl: Command not found." After Sourcing the fsl configuration I got the following messages: fslview Invalid MIT-MAGIC-COOKIE-1 keyfslview: cannot connect to X server :0 fsl No command 'fsl' found, did you mean: Command 'fsls' from package 'python-fs' (universe) Command 'fsp' from package 'alliance' (universe) Command 'psl' from package 'psl' (universe) Command 'sl' from package 'sl' (universe) Command 'fs' from package 'openafs-client' (universe) Command 'fal' from package 'dnet-progs' (universe) Command 'fsc' from package 'scala' (universe) Command 'fls' from package 'sleuthkit' (universe) Command 'wsl' from package 'wsl' (universe) fsl: command not found On Thu, Sep 8, 2016 at 9:37 AM, Parzer, Peter <[log in to unmask]<mailto:[log in to unmask]>> wrote: Source the fsl configuration file and look at the FSLDIR environment variable. It should look like this: $ . /etc/fsl/5.0/fsl.sh $ echo $FSLDIR /usr/share/fsl/5.0 What happens when you type "fsl" or "fslview" in the terminal? ________________________________ Von: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> im Auftrag von Ali Golestani <[log in to unmask]<mailto:[log in to unmask]>> Gesendet: Donnerstag, 8. September 2016 15:15 An: [log in to unmask]<mailto:[log in to unmask]> Betreff: Re: [FSL] AW: [FSL] Problem installing FSL on ubuntu 16.04 Hi Peter; I used the commands you mentioned to install FSL but it doesn't work for me. I also tried to remove it with apt-get purge fsl-complete and then install it again with apt-get install fsl-complete. I got the following messages, which suggest it is installed, but still I cannot find FSL folder at /usr/share/ or anywhere else Reading package lists... Done Building dependency tree Reading state information... Done The following NEW packages will be installed: fsl-complete 0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded. Need to get 0 B/3,982 B of archives. After this operation, 12.3 kB of additional disk space will be used. Selecting previously unselected package fsl-complete. (Reading database ... 253576 files and directories currently installed.) Preparing to unpack .../fsl-complete_5.0.7-1~nd+1+nd16.04+1_all.deb ... Unpacking fsl-complete (5.0.7-1~nd+1+nd16.04+1) ... Setting up fsl-complete (5.0.7-1~nd+1+nd16.04+1) ... On Thu, Sep 8, 2016 at 2:28 AM, Parzer, Peter <[log in to unmask]<mailto:[log in to unmask]><mailto:[log in to unmask]<mailto:[log in to unmask]>>> wrote: What are the command you used to install fsl? I installed it with the following commands and it worked fine. sudo -i wget -O- http://neuro.debian.net/lists/`lsb_release<http://neuro.debian.net/lists/lsb_release> -sc`.de-m.full -O /etc/apt/sources.list.d/neurodebian.list wget http://neuro.debian.net/_static/neuro.debian.net.asc -O - | apt-key add - apt-get update apt-get install fsl-complete If this still does not work then try to reinstall with apt-get purge fsl-complete apt-get install fsl-complete ________________________________________ Von: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> im Auftrag von Ali Golestani <[log in to unmask]<mailto:[log in to unmask]>> Gesendet: Mittwoch, 7. September 2016 17:36 An: [log in to unmask]<mailto:[log in to unmask]> Betreff: [FSL] Problem installing FSL on ubuntu 16.04 I have a problem in installing FSL on ubuntu 16.04. 1- It seems that FSL is already installed on my computer; When it try to install it I get the following message: Reading package lists... Done Building dependency tree Reading state information... Done fsl is already the newest version (5.0.9-1~nd+1+nd16.04+1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2- However, there is no FSL folder at "share" directory: /usr/share/fsl: No such file or directory. 3- I cannot find any FSL related folder on my computer. There are only some fsl files at /usr/bin/ I would appreciate it if anyone help me to fix or re-install fsl on my computer. Thanks