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Hi, On my mac I have ~/.bash_profile but neither ~/.profile or ~/.bashrc If you don’t have any of these, and a new terminal did not fix it, then create one of these and in this file place the contents that are shown in the first box here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup?highlight=%28fsl.sh%29<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup?highlight=(fsl.sh)> This should fix your problems. All the best, Mark On 25 Mar 2020, at 09:23, paul mccarthy <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Seb, It might be called ~/.profile or ~/.bashrc (I don't have a mac at hand, and can never remember which one it is). Did opening a new terminal make a difference? Paul On Mar 25 2020, at 9:19 am, Sebastian Quezada <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear Paul, It looks I don't have the file you mention, for some reason. I can see ~/.bash_history and ~/.bash_sessions in the directory, among other files, but not the one you mention. Should the FSL script have installed such file? This is not my Mac so I'm unsure whether my wife deleted the file (unlikely, she's not tech savvy), but I'm unsure why that file is missing. Can I 'restore' it? Cheers, Seb On Wed, Mar 25, 2020 at 8:06 PM paul mccarthy <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Seb, You may just need to close and re-open a terminal to ensure that your shell environment is refreshed. If this does not fix things, then check the contents of the ~/.bash_profile file to see if the FSL initialisation code has been added to it. Paul On Mar 25 2020, at 3:46 am, Sebastian Quezada Rojas <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL Community. I am new to FSL and to using MacOSX terminal and command line, and I have tried to install FSL without much success. I am using MacOS Catalina v 10.15.3 and I have installed XQuartz as recommended. I have also downloaded the most up-to-date versions of the python script and thus of FSL (6.0.3) I followed the instructions in the website (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX) and there appears to be no error while the script works (the script displays [OK] at all stages, and no warning messages are prompt). I have installed FSL in the default location (/usr/local/fsl). However, when I move onto the next stage (checking the environment is correct) and typing echo $FSLDIR The terminal returns a blank line, and when I type flirt -version it returns -bash: flirt: command not found Have I missed a previous step that is not on the website, or does my Mac need some updating of some sort? I'd really appreciate your help here. Cheers, Seb ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 -- Sebastian A. Quezada Rojas Biotechnology Engineer, MSc, PhD. Postdoctoral Fellow, NeuroDevelopment, Protection and Repair (NDPR) Laboratory, School of Health and Biomedical Sciences, RMIT University Melbourne, Australia Tel: +61 448 283 303 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1