An example script can be found in the examples folder. It is copied here as well. Preprocessing and fitting are now split into two separate functions: designer for preprocessing and tmi for fitting.
#!/bin/bash
datapath=/mnt/labspace/Projects/MESO_v2.0/ALLSUBJS_2.0/M9734
meso1=M9734_074YM_DIFF_meso.nii
meso2=M9734_074YM__DIFF_meso_research.nii
pa=M9734_074YM_DIFF_meso_PA.nii
cd $datapath
designer \
-denoise -algorithm jespersen -extent 7,7,7 \
-degibbs \
-mask \
-scratch designer2_processing_test -nocleanup \
$meso1,$meso2 designer2_test.mif
tmi \
-DTI -DKI -WDKI -SMI \
-mask designer2_processing_test/brain_mask.nii \
-sigma designer2_processing_test/sigma.nii \
-nocleanup \
designer2_test.mif designer2_params_test