FSL GUI command "fsl" Not Functioning

Software Support
1

Summary of what happened:

Downloaded FSL and it was working very well! Attempted to download miniconda3 and new error appeared (see below). I cannot launch the gui but I can run commands (fsleyes works for sure) from the command line. I am fairly new to using the terminal in such an in depth way so any help would be appreciated.

Command used (and if a helper script was used, a link to the helper script or the command generated):

Command: fsl

Version:

FSL 6.0.7.6

Environment (Docker, Singularity, custom installation):

Default Settings

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

Upon Starting Terminal:
“/Users/coriglianomic/fsl/etc/fslconf/fsl.cshsetenv: No such file or directory.”

Entering “fsl” command:
You need to source an FSL setup file - either fsl.sh or fsl.csh in $FSLDIR/etc/fslconf !

Screenshots / relevant information:

N/A

2

Hi @mcneuro, it looks like something has gone wrong with your shell configuration. What shell are you using? You should be able to find out by running this in a terminal:

echo $SHELL

3

Hi @paulmccarthy, my default shell is “/bin/tcsh”. Thank you so much for your willingness to help me through this!

4

Ok - could you run this command and paste the output here?

cat ~/.tcshrc

5

Please see below:


coriglianomic% cat ~/.tcshrc

# -------------------------------------------------------

# for AFNI: auto-inserted by init_user_dotfiles.py

# import the environment from .cshrc

source /Users/coriglianomic/.cshrc

# -------------------------------------------------------

# FSL Setup

setenv FSLDIR /Users/coriglianomic/fsl

setenv PATH ${FSLDIR}/share/fsl/bin:${PATH}

source ${FSLDIR}/etc/fslconf/fsl.cshsetenv PATH /opt/homebrew/bin:$PATH

setenv PATH /opt/homebrew/bin:$PATH

# >>> conda initialize >>>

# !! Contents within this block are managed by 'conda init' !!

if ( -f "/Users/coriglianomic/miniconda3/etc/profile.d/conda.csh" ) then

source "/Users/coriglianomic/miniconda3/etc/profile.d/conda.csh"

else

setenv PATH "/Users/coriglianomic/miniconda3/bin:$PATH"

endif

# <<< conda initialize <<<
6

It looks like homebrew is the culprit here*. Can you open this file in a text editor (e.g. nano ~/.tcshrc) and change the line:

source ${FSLDIR}/etc/fslconf/fsl.cshsetenv PATH /opt/homebrew/bin:$PATH

to:

source ${FSLDIR}/etc/fslconf/fsl.csh
setenv PATH /opt/homebrew/bin:$PATH

*I’ll also update the fslinstaller.py script so that it adds a new line to the end of the FSL configuration.

7

This worked! Thank you so much!

8

hi @paulmccarthy
Got same error and this is my .profile file in user_home
my shell is ‘/bin/bash’

# FSL Setup
FSLDIR=/home/soheil/fsl
PATH=${FSLDIR}/share/fsl/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh
9

Hi @SoheilZ, can you copy+paste all of the error messages that are printed when you open a terminal and try to run a FSL tool?