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====== Como sacar el SUVR de cualquier ROI en PET =====

El analisis PET(amiloide) actual se basa el la ROI especifica utilizada para calcular el Centiloide. No obstante, suponiendo que querramos sacar el SUVR en alguna otra ROI, tambien se puede implementar sin demasiada complejidad.

Este metodo esta basado en el nuevo pipeline para PET(tau). Solo hay que cambiar el tipo de input, las ROI y ROR y poco mas. El analisis no difire nada sea el PET que sea. :-O

===== Registro a T1w =====

<code bash apet_reg.sh>
#!/bin/sh

study=$1
shift
id=$1
shift
wdir=$1
shift
src=$1
shift

td=${wdir}'/.tmp_'${id}
if [ ! -d "$td" ]; then
        mkdir $td
fi
debug=0
${FREESURFER_HOME}/bin/mri_convert --in_type mgz --out_type nii ${SUBJECTS_DIR}/${study}_${id}/mri/rawavg.mgz ${wdir}/${id}_struc.nii.gz
${FSLDIR}/bin/fslsplit ${src} ${td}/${id}_piece_ -t
for x in ${td}/${id}_piece_*; do
        ${ANTS_PATH}/antsRegistrationSyNQuick.sh -d 3 -f ${wdir}/${id}_struc.nii.gz -m ${x} -t a -o ${x%.nii.gz}_movingToFixed_;
        ${ANTS_PATH}/antsApplyTransforms -d 3 -r ${wdir}/${id}_struc.nii.gz -i ${x} -t ${x%.nii.gz}_movingToFixed_0GenericAffine.mat -o ${x%.nii.gz}_reg.nii.gz;
done
a=`for i in ${td}/*_reg.nii.gz; do echo " $i"; done`
${FSLDIR}/bin/fslmerge -t ${td}/${id}_corr.nii.gz $a
${FSLDIR}/bin/fslmaths ${td}/${id}_corr.nii.gz -Tmean ${wdir}/${id}_pet.nii.gz
if [ $debug = 0 ] ; then
    rm -rf ${td}/*_piece_*
fi
</code>

==== Report ====

===== Mascaras =====

<code perl>

                foreach my $roi (@rois){
                        $ptask{'output'} = $outdir.'/pet_roi_'.$roi.'_'.$subject;
                        $ptask{'filename'} = $outdir.'/'.$subject.'_roi_'.$roi.'.sh';
                        $ptask{'command'} = $ENV{'PIPEDIR'}.'/bin/get_proi.sh '.$study.'_'.$subject.' '.$w_dir.'/.tmp_'.$subject.' '.$roi;
                        $mask_chain.= $w_dir.'/.tmp_'.$subject.'/rois/'.$roi.'.nii.gz ';
                        send2slurm(\%ptask);
                }
                #Hacer mascara de cerebelo
                $ptask{'output'} = $outdir.'/pet_cgm_'.$subject;
                $ptask{'filename'} = $outdir.'/'.$subject.'_cgm.sh';
                $ptask{'command'} = $ENV{'PIPEDIR'}.'/bin/get_cbgm.sh '.$study.'_'.$subject.' '.$w_dir.'/.tmp_'.$subject;
                $mask_chain.= $w_dir.'/.tmp_'.$subject.'/rois/cerebgm.nii.gz';
                send2slurm(\%ptask);
                #Juntar todas las mascaras en un 4D
                $ptask{'output'} = $outdir.'/pet_merge_'.$subject;
                $ptask{'filename'} = $outdir.'/'.$subject.'_merge.sh';
                $ptask{'command'} = $ENV{'FSLDIR'}.'/bin/fslmerge -t '.$w_dir.'/'.$subject.'_masks '.$mask_chain;
                #$ptask{'mailtype'} = 'FAIL,END';
                $ptask{'dependency'} = 'singleton';
                my $mjob_id = send2slurm(\%ptask);
</code>

<code bash get_proi.sh>
#!/bin/sh
subject=$1
shift

tmp_dir=$1
shift

roi=$1
shift

if [ ! -f ${tmp_dir}/rois/register.dat ]; then
        mkdir -p ${tmp_dir}/rois/;
        tkregister2 --mov $SUBJECTS_DIR/${subject}/mri/rawavg.mgz --noedit --s ${subject} --regheader --reg ${tmp_dir}/rois/register.dat;
        sleep 10;
fi
if [ ! -f ${tmp_dir}/all_aseg.nii.gz ]; then
        mri_label2vol --seg $SUBJECTS_DIR/${subject}/mri/aparc+aseg.mgz --temp $SUBJECTS_DIR/${subject}/mri/rawavg.mgz --o ${tmp_dir}/all_aseg.nii.gz --reg ${tmp_dir}/rois/register.dat;
        sleep 10;
fi
mkdir ${tmp_dir}/rois/${roi};
for x in `cat ${PIPEDIR}/lib/pet/${roi}.roi`; do
        sleep 10;
        rlabel=$(echo ${x} | awk -F"," '{print $1}');
        nlabel=$(echo ${x} | awk -F"," '{print $2}');
        ${FSLDIR}/bin/fslmaths ${tmp_dir}/all_aseg.nii.gz -uthr ${rlabel} -thr ${rlabel} -div ${rlabel} ${tmp_dir}/rois/${roi}/${nlabel};
done
a=$(for x in ${tmp_dir}/rois/${roi}/*.nii.gz; do echo "${x} -add "; done)
a=$(echo ${a} | sed 's/\(.*\)-add$/\1/')
${FSLDIR}/bin/fslmaths ${a} ${tmp_dir}/rois/${roi}

</code>

===== Normalizacion =====

===== PVC =====

===== Metricas =====