#!/bin/bash  

    module load afni #2022
    module load ANTs/20150828 #in our system this is ants/2.1.0
    module unload fsl #need to unload crashy version of fsl
    module load fsl/6.0.5 #not crashy version of fsl


    cd <working directory>/sub-aRi114/ #two folders, anat, dwi. 

    template="DSURQE_100micron_average.nii.gz"
    template_mask="DSURQE_100micron_mask_dilated.nii.gz"
    anat_file=/anat/"sub-aRi114_ses-1_T2w.nii.gz"
    anat2temp='anat2temp.nii.gz'
    anat2temp_inv='anat2temp_inv.nii.gz'
    anat_base=$(basename ${anat_file})
    anat_noext="$(remove_ext ${anat_base})"
    echo Anatomical file: ${anat_file}
    echo Template mask: ${template_mask}
    echo Anatomical base: ${anat_base}
    echo Anatomical noext: ${anat_noext}
    echo Anatomical anat2temp: ${anat2temp}
    echo Anatomical inverse_anat2temp: ${anat2temp_inv}




mkdir -p tmp_data/anat
cp anat/* tmp_data/anat || { echo Failed to copy files; exit 1; }
cp  * tmp_data/anat


cd tmp_data/anat


    3drefit -deoblique  -overwrite ${anat_base}
    3dresample -orient lpi -prefix ${anat_noext}'_lpi.nii.gz' -input ${anat_base}
    3dAutobox -prefix ${anat_noext}'_auto.nii.gz' -input ${anat_noext}'_lpi.nii.gz'
    N4BiasFieldCorrection -d 3 -i ${anat_noext}'_auto.nii.gz' -o ${anat_noext}'_N4.nii.gz' 
    DenoiseImage -d 3 -i ${anat_noext}'_N4.nii.gz'  -o ${anat_noext}'_N4_dn.nii.gz'
    ImageMath 3 ${anat_noext}'_N4_dn.nii.gz' TruncateImageIntensity ${anat_noext}'_N4_dn.nii.gz' 0.05 0.999

    fslmaths 'sub-aRi114_ses-1_T2w_mask.nii.gz' -kernel 3D -dilM ${anat_noext}'_mask_dilated.nii.gz'
    anat_mask=${anat_noext}'_mask_dilated.nii.gz'
    echo Anatomical mask: ${anat_mask}

mkdir -p reg
    antsRegistration --dimensionality 3 --float 0 -a 0 -v 1 --output reg/anat2std --interpolation Linear --winsorize-image-intensities [0.005,0.995] --use-histogram-matching 0 --initial-moving-transform [DSURQE_100micron_average.nii.gz,${anat_noext}'_N4_dn.nii.gz',1] --transform Rigid[0.1] --metric MI[DSURQE_100micron_average.nii.gz,${anat_noext}'_N4_dn.nii.gz',1,32,Regular,0.25] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform Affine[0.1] --metric MI[DSURQE_100micron_average.nii.gz,${anat_noext}'_N4_dn.nii.gz',1,32,Regular,0.25] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform SyN[0.1,3,0] --metric CC[DSURQE_100micron_average.nii.gz,${anat_noext}'_N4_dn.nii.gz',1,4] --convergence [30x20x10x5,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox  --masks [${template_mask},${anat_mask}]


    ComposeMultiTransform 3 ${anat2temp} -R DSURQE_100micron_average.nii.gz reg/anat2std1Warp.nii.gz reg/anat2std0GenericAffine.mat

    ComposeMultiTransform 3 ${anat2temp_inv} -R DSURQE_100micron_average.nii.gz -i reg/anat2std0GenericAffine.mat reg/anat2std1InverseWarp.nii.gz  

    antsApplyTransforms -i ${anat_noext}'_N4_dn.nii.gz' -r DSURQE_100micron_average.nii.gz -t ${anat2temp} -o ${anat_noext}'_2std.nii.gz'

slicer ${anat_noext}'_2std.nii.gz' DSURQE_100micron_average.nii.gz -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard1.png ; slicer DSURQE_100micron_average.nii.gz ${anat_noext}'_2std.nii.gz' -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard2.png ; pngappend highres2standard1.png - highres2standard2.png anat2template.png; rm -f sl?.png highres2standard2.png

    rm highres2standard1.png