#!/bin/bash

i
#convert data to MRtrix's specific format .mif
mrconvert sub-CON03/ses-preop/dwi/sub-CON03_ses-preop_acq-AP_dwi.nii.gz sub-CON03/ses-preop/dwi/CON03_AP_dwi.mif -fslgrad sub-CON03/ses-preop/dwi/sub-CON03_ses-preop_acq-AP_dwi.bvec sub-CON03/ses-preop/dwi/sub-CON03_ses-preop_acq-AP_dwi.bval -force

mrconvert sub-CON03/ses-preop/dwi/sub-CON03_ses-preop_acq-PA_dwi.nii.gz sub-CON03/ses-preop/dwi/CON03_PA_dwi.mif -fslgrad sub-CON03/ses-preop/dwi/sub-CON03_ses-preop_acq-PA_dwi.bvec sub-CON03/ses-preop/dwi/sub-CON03_ses-preop_acq-PA_dwi.bval -force


#denoising the data
dwidenoise sub-CON03/ses-preop/dwi/CON03_AP_dwi.mif sub-CON03/ses-preop/dwi/CON03_AP_denoised.mif -noise sub-CON03/ses-preop/dwi/noise_AP.mif -force

dwidenoise sub-CON03/ses-preop/dwi/CON03_PA_dwi.mif sub-CON03/ses-preop/dwi/CON03_PA_denoised.mif -noise sub-CON03/ses-preop/dwi/noise_PA.mif -force

#calculate the noise residuals
mrcalc sub-CON03/ses-preop/dwi/CON03_AP_dwi.mif sub-CON03/ses-preop/dwi/CON03_AP_denoised.mif -subtract sub-CON03/ses-preop/dwi/res_AP.mif -force

mrcalc sub-CON03/ses-preop/dwi/CON03_PA_dwi.mif sub-CON03/ses-preop/dwi/CON03_PA_denoised.mif -subtract sub-CON03/ses-preop/dwi/res_PA.mif -force

#removal of Gibbs ringing arefacts
mrdegibbs sub-CON03/ses-preop/dwi/CON03_AP_denoised.mif sub-CON03/ses-preop/dwi/CON03_AP_nogibbs.mif -force 

mrdegibbs sub-CON03/ses-preop/dwi/CON03_PA_denoised.mif sub-CON03/ses-preop/dwi/CON03_PA_nogibbs.mif -force  

#distrotion correction and preprocessing with dwifslpreproc

#extract one b0 volume from the AP and the PA datasets, and concatenate the two
mrconvert sub-CON03/ses-preop/dwi/CON03_AP_nogibbs.mif -coord 3 1 sub-CON03/ses-preop/dwi/b0_AP.mif -force

mrconvert sub-CON03/ses-preop/dwi/CON03_PA_nogibbs.mif -coord 3 1 sub-CON03/ses-preop/dwi/b0_PA.mif -force

mrcat sub-CON03/ses-preop/dwi/b0_AP.mif sub-CON03/ses-preop/dwi/b0_PA.mif -axis 3 sub-CON03/ses-preop/dwi/b0_pair.mif -force


#run dwifslpreproc
dwipreproc sub-CON03/ses-preop/dwi/CON03_AP_nogibbs.mif sub-CON03/ses-preop/dwi/CON03_preproc.mif -pe_dir AP -rpe_pair -se_epi sub-CON03/ses-preop/dwi/b0_pair.mif -readout_time 0.0266 -align_seepi -eddy_options " --slm=linear" -force


#generate a brain mask for subsequent analyses

#first apply bias correction using dwibiascorrect
dwibiascorrect sub-CON03/ses-preop/dwi/CON03_preproc.mif sub-CON03/ses-preop/dwi/CON03_preproc_unbiased.mif -bias sub-CON03/ses-preop/dwi/bias.mif -ants -force

dwi2mask sub-CON03/ses-preop/dwi/CON03_preproc_unbiased.mif sub-CON03/ses-preop/dwi/dwi_brain_mask.mif -force