I am trying to install the FSL software on my computer. For that I downloaded the .ebuild files from
Gentoo Portage Overlays - sci-biology/fsl
and used the standard gentoo installation command
emerge sci-biology/fsl
The installation process failed with a complain about the “giftiio” library, see the attached screenshot. Any help with resolving this failure is appreciated.
Hi @artan, the official instructions for installing FSL can be found at FSL - the FMRIB Software Library - the FSL team has nothing to do with this Gentoo overlay, which looks severely out-dated and probably unmaintained.
Hi Paul,
Thank you for helping. I downloaded the FSL package from the link you provided. The installation finished without errors. Now, when I try to start the fsl from the command line it produces this output:
Hi @artan, what shell are you using? Can you confirm that your shell profile has been configured correctly? E.g. share the output of running env (or the equivalent in whatever shell you are using)?
Hi Paul,
Here is the env in my shell:
SHELL=/bin/bash
SESSION_MANAGER=local/parrot:@/tmp/.ICE-unix/3411,unix/parrot:/tmp/.ICE-unix/3411
WINDOWID=52
COLORTERM=truecolor
XDG_CONFIG_DIRS=/home/xxxxx/.config/kdedefaults:/etc/xdg
LESS=-R -M --shift 5
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session1
XDG_MENU_PREFIX=plasma-
JDK_HOME=/etc/java-config-2/current-system-vm
CONFIG_PROTECT_MASK=/etc/sandbox.d /etc/php/cli-php8.2/ext-active/ /etc/php/cgi-php8.2/ext-active/ /etc/php/apache2-php8.2/ext-active/ /etc/php/fpm-php8.2/ext-active/ /etc/php/phpdbg-php8.2/ext-active/ /etc/fonts/fonts.conf /etc/gentoo-release /etc/terminfo /etc/dconf /etc/ca-certificates.conf /etc/texmf/web2c /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/revdep-rebuild
R_HOME=/usr/lib64/R
PYCHARM_JDK=/etc/java-config-2/current-system-vm
ICEAUTHORITY=/run/user/1000/iceauth_faEdKW
LANGUAGE=
JAVA_HOME=/etc/java-config-2/current-system-vm
SHELL_SESSION_ID=2e8f94a1518246d29229925ce95bbff2
FSLWISH=/usr/local/fsl/bin/fslwish
ANT_HOME=/usr/share/ant
DESKTOP_SESSION=plasma
GTK_RC_FILES=/etc/gtk/gtkrc:/home/xxxxx/.gtkrc:/home/xxxxx/.config/gtkrc
EDITOR=/bin/nano
XDG_SEAT=seat0
PWD=/home/xxxxx
CONFIG_PROTECT=/var/bind /usr/share/gnupg/qualified.txt /usr/share/config /usr/lib64/libreoffice/program/sofficerc
LOGNAME=xxxxx
XDG_SESSION_TYPE=wayland
MANPATH=/etc/java-config-2/current-system-vm/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/14/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.44/man:/etc/java-config-2/current-system-vm/man/:/usr/lib64/php8.2/man/:/usr/local/share/man:/usr/share/man:/usr/lib/rust/man-1.84.1:/usr/lib/llvm/19/share/man:/usr/lib/llvm/18/share/man:/usr/lib/llvm/15/share/man
TCLLIBPATH= "/usr/local/lib64/KWWidgets/tcl" "/usr/lib64/bwidget-1.9.8" "/usr/lib64/tcltk/vtk-7.1" "/usr/lib64"
XAUTHORITY=/run/user/1000/xauth_luYcWo
OPENCL_PROFILE=ocl-icd
MOTD_SHOWN=pam
GTK2_RC_FILES=/etc/gtk-2.0/gtkrc:/home/xxxxx/.gtkrc-2.0:/home/xxxxx/.config/gtkrc-2.0
HOME=/home/xxxxx
SSH_ASKPASS=/usr/bin/ksshaskpass
LANG=en_US.utf8
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:su=37;41:sg=30;43:ca=00:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.7z=01;31:*.ace=01;31:*.alz=01;31:*.apk=01;31:*.arc=01;31:*.arj=01;31:*.bz=01;31:*.bz2=01;31:*.cab=01;31:*.cpio=01;31:*.crate=01;31:*.deb=01;31:*.drpm=01;31:*.dwm=01;31:*.dz=01;31:*.ear=01;31:*.egg=01;31:*.esd=01;31:*.gz=01;31:*.jar=01;31:*.lha=01;31:*.lrz=01;31:*.lz=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.lzo=01;31:*.pyz=01;31:*.rar=01;31:*.rpm=01;31:*.rz=01;31:*.sar=01;31:*.swm=01;31:*.t7z=01;31:*.tar=01;31:*.taz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tgz=01;31:*.tlz=01;31:*.txz=01;31:*.tz=01;31:*.tzo=01;31:*.tzst=01;31:*.udeb=01;31:*.war=01;31:*.whl=01;31:*.wim=01;31:*.xz=01;31:*.z=01;31:*.zip=01;31:*.zoo=01;31:*.zst=01;31:*.avif=01;35:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.cfg=00;32:*.conf=00;32:*.diff=00;32:*.doc=00;32:*.ini=00;32:*.log=00;32:*.patch=00;32:*.pdf=00;32:*.ps=00;32:*.tex=00;32:*.txt=00;32:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:*~=00;90:*#=00;90:*.bak=00;90:*.crdownload=00;90:*.dpkg-dist=00;90:*.dpkg-new=00;90:*.dpkg-old=00;90:*.dpkg-tmp=00;90:*.old=00;90:*.orig=00;90:*.part=00;90:*.rej=00;90:*.rpmnew=00;90:*.rpmorig=00;90:*.rpmsave=00;90:*.swp=00;90:*.tmp=00;90:*.ucf-dist=00;90:*.ucf-new=00;90:*.ucf-old=00;90:
XDG_CURRENT_DESKTOP=KDE
KONSOLE_DBUS_SERVICE=:1.46
WAYLAND_DISPLAY=wayland-0
KONSOLE_DBUS_SESSION=/Sessions/2
PROFILEHOME=
OPENGL_PROFILE=xorg-x11
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
FSLDIR=/usr/local/fsl
QT_GRAPHICSSYSTEM=raster
KONSOLE_VERSION=241203
GTK_MODULE=/usr/lib64/gtk-2.0/modules/
KDE_SESSION_UID=1000
INFOPATH=/usr/share/gcc-data/x86_64-pc-linux-gnu/14/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.44/info:/usr/share/autoconf-2.72/info:/usr/share/autoconf-2.13/info:/usr/share/automake-1.17/info:/usr/share/info
JAVAC=/etc/java-config-2/current-system-vm/bin/javac
XDG_SESSION_CLASS=user
TERM=xterm-256color
LESSOPEN=|lesspipe %s
USER=xxxxx
FSLTCLSH=/usr/local/fsl/bin/fsltclsh
COLORFGBG=15;0
QT_WAYLAND_RECONNECT=1
KDE_SESSION_VERSION=6
PAM_KWALLET5_LOGIN=/run/user/1000/kwallet5.socket
MANPAGER=manpager
DISPLAY=:1
SHLVL=1
PAGER=/usr/bin/less
LEX=flex
XDG_VTNR=7
XDG_SESSION_ID=2
FSLMULTIFILEQUIT=TRUE
FSL_LOAD_NIFTI_EXTENSIONS=0
LD_LIBRARY_PATH=/usr/local/lib:/usr/local/lib64:/usr/local/qwt6.3/lib:
XDG_RUNTIME_DIR=/run/user/1000
GCC_SPECS=
GSETTINGS_BACKEND=dconf
QT_AUTO_SCREEN_SCALE_FACTOR=0
XDG_DATA_DIRS=/usr/local/share:/usr/share
KDE_FULL_SESSION=true
PATH=/usr/local/fsl/share/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/lib/llvm/19/bin:/usr/lib/llvm/18/bin:/usr/lib/llvm/15/bin
FSL_SKIP_GLOBAL=0
DBUS_SESSION_BUS_ADDRESS=unix:path=/tmp/dbus-gxxqOpofAB,guid=e47e0ac089b1c7df56be9023680a2d02
KDE_APPLICATIONS_AS_SCOPE=1
MAIL=/var/mail/xxxxx
SHELL_SETS_TITLE=0
FSLOUTPUTTYPE=NIFTI_GZ
KONSOLE_DBUS_WINDOW=/Windows/7
_=/usr/bin/env
Can you try running unset TCLLIBPATH, and then running fsl?
Hi Paul,
Ok, that did the trick. Do I need to add something fsl specific in front of TCLLIBPATH in my .bashrc?
Hi @artan, ultimately the problem is with whatever other software you are using which requires the $TCLLIBPATH variable to be set. This variable is for use in development, similar to LD_LIBRARY_PATH, PYTHONPATH, etc, and should generally not be used on end-user/production installations.
But you might be able to force FSL to ignore it by modifying your copy of $FSLDIR/bin/Runtcl, adding set auto_path {} before the source ... line near the bottom, i.e.:
...<beginning of script>...
set auto_path {}
source ${FSLDIR}/tcl/${origname}.tcl
exit
Thank you, Paul for also providing the way to go around the namespace collision in my shell. Made my day easier. 
The FSL installation is working alright with the fMRI example data. Now I have encountered an error when trying to test run the ASL data
I don’t know where to start debugging this problem.
I found the solution from a post of Paul in 2021. The solution is to edit $FSLDIR/bin/asl_gui and add
import os
os.environ["GDK_BACKEND"]="x11"
Hi Paul,
I followed the process given in FSL installation page, I am trying to install the software in windows and I have tried with Ubuntu 22.04 terminal, but below is the error I got:
shreyansh@DESKTOP-MONTLKN:/mnt/c/Users/LEGION/Downloads$ python3 fslinstaller.py
FSL installer version: 3.17.0
Press CTRL+C at any time to cancel installation
Installation log file: /tmp/fslinstaller_3ltpj7pb.log
Installing FSL implies agreement with the terms of the FSL license - if you do not agree with these terms, you can
cancel the installation by pressing CTRL+C. You can view the license at https://fsl.fmrib.ox.ac.uk/fsl/docs/license.html
During the installation process, please note that some system details will be automatically sent to the FSL
development team. These details are extremely basic and cannot be used in any way to identify individual users.
If you do not want any information to be sent, please cancel this installation by pressing CTRL+C, and re-run the installer with the --skip_registration option.
FSL 6.0.7.19 selected for installation
Where do you want to install FSL?
Press enter to install to the default location [/home/shreyansh/fsl]
FSL installation directory [/home/shreyansh/fsl]:
Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.19_linux-64.yml...
Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.19_osl-dynamics_linux-64.yml...
Downloading FSL environment specification from https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fsl-6.0.7.19_truenet_linux-64.yml...
Installing FSL in /home/shreyansh/fsl
Downloading miniconda from https://anaconda.org/conda-forge/micromamba/2.1.0/download/linux-64/micromamba-2.1.0-0.tar.bz2...
ERROR occurred during installation!
<urlopen error [Errno 104] Connection reset by peer>
FSL installation failed!
Please check the log file - it may contain some more information to help you diagnose the problem: /home/shreyansh/fsl_installation_20260114011451.log
Here is the log file I have:
fsl_installation_20260112124810.txt (25.3 KB)
Please help me to resolve this issue.
Hi @SHREYANSH_FAYE, it looks like the network connection was interrupted - can you try again? Use the most reliable internet connection that you have available to you.
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