Fsleyes errors (docker toolbox + sct vers 4.2.1)

I’m using sct with docker toolbox since I have a Windows 10 and everytime I open fsleyes I get this message: The $FSLDIR environment variable is not set - FSLeyes may not behave correctly ( Locate $FSLDIR or Skip )

While I was trying to use fsleyes I’ve noticed two other things:

  • I can’t save the image after modifying it manually ( if i go to overlay the “save” button doesn’t work)
  • I can’t use properly the integration with sct ( I can open the sct_plugin.py , but when for example I try to use deepseg and I push the button “spinal cord segmentation” nothing happens.

Are this latter things related with the first error ( FSLDIR…)?

Thank you for your help


Thank you for your feedback and sorry about this error. We were able to reproduce it, and a ticket has been opened. We are working on a solution.


This issue is now fixed in SCT’s development version (git-master) and will be available in the next v4.2.2 release.