#!/bin/sh                                                                                                                                                                
 
Usage() {                                                                                                                                                                
    echo ""                                                                                                                                                              
    echo "Usage: dti_bedtrack.sh  <project> <name> <working dir>"                                                                                                          
    echo ""                                                                                                                                                              
    echo "You must have FSL installed in order to run this script"                                                                                                       
    echo ""                                                                                                                                                              
    exit 1                                                                                                                                                               
}                                                                                                                                                                        
 
[ "$3" = "" ] && Usage
debug=1
prj=$1
shift
pollo=$1
shift
w_dir=$1
shift
td=${w_dir}'/.tmp_'${pollo}
bd=${td}'/bedpostx'
if [ ! -d "$bd" ]; then                                                                                                                                                  
        mkdir $bd                                                                                                                                                        
fi 
${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
${FSLDIR}/bin/bedpostx_gpu ${bd}
${PIPEDIR}/bin/get_aseg.sh ${prj} ${pollo} ${w_dir}
WarpImageMultiTransform 3 ${w_dir}/${pollo}_aseg.nii.gz ${td}/${pollo}_aseg_warped.nii.gz -R ${td}/hifi_b0.nii.gz ${td}/${pollo}_dti_ants_elast_t1_b0Warp.nii.gz ${td}/${pollo}_dti_ants_elast_t1_b0Affine.txt
########################################################
######## Falta calcular las mascaras para seeds ########
########################################################
probtrackx2 --opd --forcedir -s ${bd}.bedpostX/merged -m ${w_dir}/${pollo}_dti_brain_mask -x ${td}/${pollo}_tmp_mask --dir=\'${td}/probtrack_out\'