ERROR FSLDIR is not set BATMAN tutorial step 2.4

1

Hi everyone,

For my research internship I would like to use MRtrix. MRtrix is totally new for me, so to get familiar with the MRtrix environment I’m currently doing the BATMAN tutorial (which is great by the way!). For the eddy-current correction (step 2.4) I typed the following command: dwipreproc dwi_den_unr.mif dwi_den_unr_preproc.mif –pe_dir AP –rpe_pair –se_epi b0_pair.mif –eddy_options “ --slm=linear”

The following error occured: [ERROR] Environment variable FSLDIR is not set; please run appropriate FSL configuration script

Does anyone have a clue on how to fix this? I’m aware of the fact that I can continue making the tutorial by using the supplementary files, but still I would like to be able to perform this correction step.

Thanks in advance!
Rianne

2

Hi Rianne,

Looks like your FSL environment is not set.

Add these lines to your bash profile:

FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

Then open a new terminal.

If it still doesn’t work then it’s likely your FSL has been installed in a different directory e.g. /usr/share/fsl

Regards,

Jerome

3

Hi Jerome,

Thanks a lot for your reply! FSL needed an update; it works now :slight_smile:

Regards,
Rianne