I am using VMware Workstation Player 16 on a Windows computer to run FSL. I am trying to view and analyze MRI’s for a research project with an old professor. I have the files on FSL but when I try to view them in the directory [fsluser@localhost fsl] using fsleyes (file name “anat.nii”) I get an error that says
bash: fsleyes: command not found
I have also tried fslview and fslview_deprecated to no avail, but these are old commands to my understanding anyway.
So, my first question is: Is fsleyes a VMware Tool? If so, I have tried to install VMware Tools and seem to have been successful, but then when I try to configure VMware Tools, I get stopped when it asks me where my gcc file is because I cannot find it.
That would lead me to my second question if that is the case: How can I find my gcc file? I have tried whereis gcc, which gcc, etc. with no luck.
If fsleyes is not a VMware Tool so that problem shouldn’t be affecting this, then what else am I missing for the command to not be found?
Thanks in advance! Happy to provide other info for context if necessary.
I would suggest installing FSL (and therefore FSLeyes) on a Windows computer using Windows Subsystem for Linux (WSL). The instructions (with a video) are here.
Alternatively, you could install FSL on a Windows machine using a Linux virtual machine, e.g. VMware Player or VirtualBox. If you follow this approach, you will want to install FSL (and therefore FSLeyes) using the standard Linux instructions. VMware Player and VirtualBox can be finicky about OpenGL applications like FSLeyes. If you have issues you can try the simple programs glxinfo and glxgears to help troubleshoot.
If you simply want to view MRI images, you may want to look at MRIcroGL which is available natively for Windows, macOS and Linux. This means you do not need WSL or a virtual machine. The Scripting/Templates menu items illustrate some of the potential for this viewer.
Hi Chris! Thanks for your response. I had originally tried to install FSL through WSL with those exact instructions, but spent days upon days troubleshooting and never was successful. I kept getting stuck at different points and eventually gave up to try it through VMware Player instead. It works for the most part, but I cannot use FSLeyes. I will try those commands and see if I can find the problem. Unfortunately I need to do more than just view the MRI’s, but thank you for the suggestion.
To be clear, I don’t need to go through all of the VMware tool configuration to use FSLeyes? The two are not necessarily related? Just want to figure out where I need to focus my attention troubleshooting.