#!/bin/sh                                                                                                                                                                
                                                                                                                                                                         
Usage() {                                                                                                                                                                
    echo ""                                                                                                                                                              
    echo "Usage: dti_bedtrack.sh  <project> <name> <working dir> <network dir>"                                                                                          
    echo ""                                                                                                                                                              
    echo "You must have FSL installed in order to run this script"                                                                                                       
    echo ""                                                                                                                                                              
    exit 1                                                                                                                                                               
}                                                                                                                                                                        
                                                                                                                                                                         
[ "$4" = "" ] && Usage                                                                                                                                                   
debug=1                                                                                                                                                                  
prj=$1                                                                                                                                                                   
shift                                                                                                                                                                    
pollo=$1                                                                                                                                                                 
shift                                                                                                                                                                    
w_dir=$1                                                                                                                                                                 
shift                                                                                                                                                                    
net_dir=$1                                                                                                                                                               
shift                                                                                                                                                                    
td=${w_dir}'/.tmp_'${pollo}                                                                                                                                              
bd=${td}'/bedpostx'                                                                                                                                                      
list=${w_dir}/../masks.list                                                                                                                                              
if [ ! -d "$bd" ]; then                                                                                                                                                  
mkdir $bd                                                                                                                                                                
fi                                                                                                                                                                       
echo "Copying files"                                                                                                                                                     
${FSLDIR}/bin/imcp ${w_dir}/${pollo}_dti_data ${bd}/data                                                                                                                 
${FSLDIR}/bin/imcp ${w_dir}/${pollo}_dti_brain_mask ${bd}/nodif_brain_mask                                                                                               
cp ${td}/bvecs ${bd}/bvecs                                                                                                                                               
cp ${td}/bvals ${bd}/bvals                                                                                                                                               
echo "Making bedpostx"                                                                                                                                                   
echo [`date`]                                                                                                                                                            
${FSLDIR}/bin/bedpostx_gpu ${bd}                                                                                                                                         
echo "So far, so good"                                                                                                                                                   
echo [`date`]
###########################################                                                                                                                              
echo "Getting nodes and making masks"                                                                                                                                    
for x in `find ${net_dir} -name "*.nii"`; do                                                                                                                             
        node=$(basename $x)                                                                                                                                              
        WarpImageMultiTransform 3 ${x} ${td}/${node%.nii.gz}_warped.nii.gz -R ${w_dir}/${pollo}_t1_reoriented.nii.gz ${td}/${pollo}_dti_ants_elast_mni_t1Warp.nii.gz ${td}/${pollo}_dti_ants_elast_mni_t1Affine.txt;                                                                                                                              
        WarpImageMultiTransform 3 ${td}/${node%.nii.gz}_warped.nii.gz ${td}/${pollo}_${node}.gz -R ${td}/hifi_b0.nii.gz ${td}/${pollo}_dti_ants_elast_t1_b0Warp.nii.gz ${td}/${pollo}_dti_ants_elast_t1_b0Affine.txt;                                                                                                                             
        echo "${td}/${pollo}_${node}.gz" >> ${td}/${pollo}_mask.list;                                                                                                    
done                                                                                                                                                                     
###########################################                                                                                                                              
echo "Doing probtrackx"                                                                                                                                                  
probtrackx2 --opd --forcedir -s ${bd}.bedpostX/merged -m ${w_dir}/${pollo}_dti_brain_mask -x ${td}/${pollo}_mask.list --dir=${td}/probtrack_out                          
rm ${td}/${pollo}_mask.list;                                                                                                                                             
echo "Done"                                                                                                                                                              
echo [`date`]