#!/bin/sh                                                                                                                                                                
 
Usage() {                                                                                                                                                                
    echo ""                                                                                                                                                              
    echo "Usage: dti_proc_nocorr.sh  <name> <T1> <input> <output_dir>"                                                                                                          
    echo ""                                                                                                                                                              
    echo "You must have FSL installed in order to run this script"                                                                                                       
    echo ""                                                                                                                                                              
    exit 1                                                                                                                                                               
}                                                                                                                                                                        
 
[ "$4" = "" ] && Usage                                                                                                                                                   
debug=1                                                                                                                                                                  
in=`${FSLDIR}/bin/remove_ext $1`                                                                                                                                         
shift                                                                                                                                                                    
t1=`${FSLDIR}/bin/remove_ext $1`                                                                                                                                         
shift                                                                                                                                                                    
b_in=$1                                                                                                                                                                  
shift                                                                                                                                                                    
out=`${FSLDIR}/bin/remove_ext $1`                                                                                                                                        
shift                                                                                                                                                                    
td=${out}'/.tmp_'${b_in}                                                                                                                                                 
#p2a=$(dirname ${in}.nii.gz)'/'${b_in}'_p2a_b0'                                                                                                                           
if [ ! -d "$td" ]; then                                                                                                                                                  
        mkdir $td                                                                                                                                                        
fi                                                                                                                                                                       
if [ ! -d "$out" ]; then                                                                                                                                                 
        mkdir $out                                                                                                                                                       
fi                                                                                                                                                                       
echo "DTI preproccessing begins ..."                                                                                                                                     
echo [`date`]                                                                                                                                                            
echo                                                                                                                                                                     
#echo "Preparing topup"                                                                                                                                                   
#${FSLDIR}/bin/imcp ${p2a} ${td}/                                                                                                                                         
${FSLDIR}/bin/fslroi $in ${td}/a2p_b0 0 1                                                                                                                                
#${FSLDIR}/bin/fslmerge -t ${td}/a2p_p2a_b0 ${td}/a2p_b0 ${td}/${b_in}_p2a_b0
#echo "Running topup"            
#${FSLDIR}/bin/topup --imain=${td}/a2p_p2a_b0 --datain=${out}/../acqparams.txt --out=${td}/topup_results --iout=${td}/hifi_b0                                             
${FSLDIR}/bin/fslmaths ${td}/a2p_b0 -Tmean ${td}/hifi_b0                                                                                                                
${FSLDIR}/bin/bet ${td}/hifi_b0 ${td}/hifi_b0_brain -m                                                                                                                   
#${FSLDIR}/bin/applytopup --imain=${in} --inindex=1 --datain=${out}/../acqparams.txt --topup=${td}/topup_results --out=${td}/${b_in}_hifi --method=jac                    
echo "Copying files for ${b_in} to ${td}/"                                                                                                                               
echo                                                                                                                                                                     
#cp ${in}.bval ${td}/bvals
#cp ${in}.bvec ${td}/bvecs
echo "Doing correction on ${td}/${b_in}_hifi"                                                                                                                            
echo [`date`]
echo                                                                                                                                                                     
#${FSLDIR}/bin/eddy_correct ${td}/${b_in}_hifi ${td}/data 0                                           
${FSLDIR}/bin/eddy_cuda --imain=${in} --mask=${td}/hifi_b0_brain --acqp=${out}/../acqparams.txt --index=dti_index.txt --bvecs=${in}.bvec --bvals=${in}.bval --out=${td}/data
echo "Running dtifit on ${td}/data"                                                                                                                                      
echo [`date`]
echo                                                                                                                                                                     
${FSLDIR}/bin/dtifit --data=${td}/data --out=${td}/dti --mask=${td}/hifi_b0_brain --bvecs=${in}.bvec  --bvals=${in}.bval
echo "I will copy all output files to ${out}/${b_in}_XXXXX"                                                                                                              
echo                                                                                                                                                                     
for x in ${td}/dti*; do ${FSLDIR}/bin/imcp ${x} ${out}/${b_in}_$(basename $x); done;                                                                                     
${FSLDIR}/bin/imcp ${td}/hifi_b0_brain ${out}/${b_in}_dti_brain_mask                                                                                                     
${FSLDIR}/bin/imcp ${td}/data ${out}/${b_in}_dti_data                                                                                                                    
echo "I need the T1 image"                                                                                                                                               
${FSLDIR}/bin/fslreorient2std ${t1} ${out}/${b_in}_t1_reoriented                                                                                                             
echo "Calculating transformation from MNI to T1"                                                                                                                         
echo [`date`]
echo
ANTS 3 -m CC[${out}/${b_in}_t1_reoriented.nii.gz, ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz, 1, 4] -r Gauss[0,3] -t Elast[1.5] -i 30x20x10 -o ${td}/${b_in}_dti_ants_elast_mni_t1.nii.gz                                                                                                                                                       
echo "Calculating transformation from T1 to B0"                                                                                                                          
echo [`date`]
echo
ANTS 3 -m CC[${td}/hifi_b0.nii.gz, ${out}/${b_in}_t1_reoriented.nii.gz, 1, 4] -r Gauss[0,3] -t Elast[1.5] -i 30x20x10 -o ${td}/${b_in}_dti_ants_elast_t1_b0.nii.gz       
echo "Applying transformations to JHU Atlas"                                                                                                                             
WarpImageMultiTransform 3 ${FSLDIR}/data/atlases/JHU/JHU-ICBM-labels-1mm.nii.gz ${td}/JHU_labels_warped_tmp.nii.gz -R ${out}/${b_in}_t1_reoriented.nii.gz ${td}/${b_in}_dti_ants_elast_mni_t1Warp.nii.gz ${td}/${b_in}_dti_ants_elast_mni_t1Affine.txt                                                                                            
WarpImageMultiTransform 3 ${td}/JHU_labels_warped_tmp.nii.gz ${td}/JHU_labels_custom_tmp.nii.gz -R ${td}/hifi_b0.nii.gz ${td}/${b_in}_dti_ants_elast_t1_b0Warp.nii.gz ${td}/${b_in}_dti_ants_elast_t1_b0Affine.txt                                                                                                                                
echo "Game over :-P"
echo [`date`]
exit 0