I am working on juptyter notebook in my VSCODE and when I try to run a command line in a cell as the following:
!'directory of fsl software' -I 'path of the mask in the MNI space' -o 'path of output file -w 'path of transformation from MNI to subjects mask' -r 'path of subject mask' --interp=nn
However, when I run the code, I obtain the error:
ERROR:: Environment variable FSLOUTPUTTYPE is not set! Please make sure that the appropriate configuration file is sourced by your shell (e.g. by putting it in .profile). e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh" e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh"
As it indicates, I open on VSC the file .bash_profile in the editor and copy:
FSLDIR=/usr/local/fsl . ${FSLDIR}/etc/fslconf/fsl.sh PATH=${FSLDIR}/bin:${PATH} export FSLDIR PATH
and, after saving the .bash_profile file and re running the line, it still doesn't work. Any idea?
I downloaded the Conda package of fslpy but I didn't use it because I'm running a command line and also I checked the dimensions of the files I was working with and that's not either the problem. I tried to download the VSCode extension in the remote server I am working with of FSharo fsl and fsy but obtained no results
