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Problemas con el procesamiento de FBB y como no morir en el intento
de DICOM a NiFTI
Necesitamos convertir los DICOM de FBB a formato NiFTI-1 para trabajar con FSL. El servidor DICOM corta el numero de slices por directorio a 500 por lo que inicialmente hubo muchisimos problemas de conversion y procesamiento.
Luego hay que buscar por todas las subcarpetas del DICOM las imagenes 4x5min que estan desordenadas. Para convertir uno de los sujetos ha de hacerse algo asi,
$ for x in `find /nas/raw_images/facehbi/fbb/FACEHBI-F001B/DICOM/ -type f`; do if [[ `dckey -k "SeriesDescription" $x 2>&1 | grep "4x5min"` ]]; then cp $x /nas/facehbi/tmp_2nifti/; fi; done; y=$(ls /nas/facehbi/tmp_2nifti/ | head -n 1); dcm2nii -o /nas/facehbi/tmp/ /nas/facehbi/tmp_2nifti/$y;
que da una salida muy ruidosa, pero funciona. Para hacerlos todos de una tacada habria que iterar esto por todos los sujetos.
for s in `ls -d /nas/clinic/* | grep FACEHBI | grep "B$"`; do sbj=$(echo $s |sed 's/.*-F\(.*\)B$/\1/'); for x in `find ${s}/DICOM/ -type f`; do if [[ `dckey -k "SeriesDescription" $x 2>&1 | grep "4x5min"` ]]; then cp $x /nas/facehbi/tmp_2nifti/; fi; done; y=$(ls /nas/facehbi/tmp_2nifti/ | head -n 1); dcm2nii -o /nas/facehbi/tmp/ /nas/facehbi/tmp_2nifti/$y; conv=$(ls /nas/facehbi/tmp/ | head -n 1); fslsplit /nas/facehbi/tmp/${conv} /nas/facehbi/fbb_first/smc0${sbj}s -t; rm -rf /nas/facehbi/tmp/*; rm -rf /nas/facehbi/tmp_2nifti/*; done
Correccion de movimiento
Ahora tenemos 4 archivos representando la integracion de 5 min y hay que corregistrarlos al espacio de usuario. Lo primero es traer el archivo de freesurfer y luego corregistrar cada uo de los fbb al user space. despues se ha de unirlos temporalmente y hacer un mcflirt.
lo primero seria traerse la mri del directorio de freesurfer
get_fs_subj
- get_fs_subj.sh
#!/bin/sh
study=$1
shift
id=$1
shift
dir=$1
shift
debug=0
#First get the freesurfer processed MRIs
${FREESURFER_HOME}/bin/mri_vol2vol --mov ${SUBJECTS_DIR}/${study}_${id}/mri/nu.mgz --targ ${SUBJECTS_DIR}/${study}_${id}/mri/rawavg.mgz --regheader --o ${dir}/${id}_tmp_nu_in_rawavg.mgz
${FREESURFER_HOME}/bin/mri_convert --in_type mgz --out_type nii ${dir}/${id}_tmp_nu_in_rawavg.mgz ${dir}/${id}_tmp.nii.gz
${FSLDIR}/bin/fslreorient2std ${dir}/${id}_tmp ${dir}/${id}_struc
${FREESURFER_HOME}/bin/mri_vol2vol --mov ${SUBJECTS_DIR}/${study}_${id}/mri/brain.mgz --targ ${SUBJECTS_DIR}/${study}_${id}/mri/rawavg.mgz --regheader --o ${dir}/${id}_tmp_brain_in_rawavg.mgz
${FREESURFER_HOME}/bin/mri_convert --in_type mgz --out_type nii ${dir}/${id}_tmp_brain_in_rawavg.mgz ${dir}/${id}_tmp_brain.nii.gz
${FSLDIR}/bin/fslreorient2std ${dir}/${id}_tmp_brain ${dir}/${id}_brain
if [ $debug = 0 ] ; then
rm ${dir}/${id}_tmp*
fi
y luego corregistrar cada imagen al espacio del sujeto. Hay 4 variantes para esto.
1.- Intentando registrar cada imagen independientemente.
fbb_reg
- fbbtemp_reg.sh
#!/bin/sh
study=$1
shift
id=$1
shift
tdir=$1
shift
wdir=$1
shift
debug=1
#get the uncorrected PETs and register to user space MRI
for i in {0..3}; do
tf=`printf "${id}s%04d" $i`
${FSLDIR}/bin/imcp ${tdir}/${tf} ${tdir}/${id}_tmp
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${id}_tmp -omat ${tdir}/${tf}_pet2struc.mat -out ${tdir}/${tf}_reg
done
a=`for i in {0..3}; do printf " ${tdir}/${id}s%04d_reg " $i; done`
${FSLDIR}/bin/fslmerge -t ${wdir}/${id}_tmp_mvc $a
${FSLDIR}/bin/mcflirt -in ${wdir}/${id}_tmp_mvc -out ${wdir}/${id}_tmp_corr
${PIPEDIR}/bin/4dmean.pl ${wdir}/${id}_tmp_corr
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${wdir}/${id}_mean -omat ${wdir}/${id}_fbb2struc.mat -out ${wdir}/${id}_fbb
if [ $debug = 0 ] ; then
rm ${tdir}/${id}_tmp*
rm ${wdir}/${id}_tmp*
fi
2.- Usando la informacion de un registro para el resto
fbb_regc
- fbbtemp_regc.sh
#!/bin/sh
study=$1
shift
id=$1
shift
tdir=$1
shift
wdir=$1
shift
sok=$1
shift
debug=1
#Now get the uncorrected PETs and register to user space MRI
bsc=`printf "${id}s%04d" $sok`
${FSLDIR}/bin/imcp ${tdir}/${bsc} ${tdir}/${id}_tmp
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${id}_tmp -omat ${tdir}/${bsc}_pet2struc.mat -out ${tdir}/${bsc}_reg
for i in {0..3}; do
if [ "$i" != "$sok" ]; then
tf=`printf "${id}s%04d" $i`
${FSLDIR}/bin/imcp ${tdir}/${tf} ${tdir}/${id}_tmp
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${id}_tmp -init ${tdir}/${bsc}_pet2struc.mat -omat ${tdir}/${tf}_pet2struc.mat -out ${tdir}/${tf}_reg
fi
done
a=`for i in {0..3}; do printf " ${tdir}/${id}s%04d_reg " $i; done`
${FSLDIR}/bin/fslmerge -t ${wdir}/${id}_tmp_mvc $a
${FSLDIR}/bin/mcflirt -in ${wdir}/${id}_tmp_mvc -out ${wdir}/${id}_tmp_corr
${PIPEDIR}/bin/4dmean.pl ${wdir}/${id}_tmp_corr
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${wdir}/${id}_mean -omat ${wdir}/${id}_fbb2struc.mat -out ${wdir}/${id}_fbb
if [ $debug = 0 ] ; then
rm ${tdir}/${id}_tmp*
rm ${wdir}/${id}_tmp*
fi
3.- Usando la informacion solo del cerebro extraido para hacer el corregistro
fbb_regb
- fbbtemp_regb.sh
#!/bin/sh
study=$1
shift
id=$1
shift
tdir=$1
shift
wdir=$1
shift
sok=$1
shift
debug=1
#Now get the uncorrected PETs and register to user space MRI
bsc=`printf "${id}s%04d" $sok`
${FSLDIR}/bin/imcp ${tdir}/${bsc} ${tdir}/${id}_tmp
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_brain -in ${tdir}/${id}_tmp -omat ${tdir}/${bsc}_pet2struc.mat -out ${tdir}/${bsc}_reg
for i in {0..3}; do
if [ "$i" != "$sok" ]; then
tf=`printf "${id}s%04d" $i`
${FSLDIR}/bin/imcp ${tdir}/${tf} ${tdir}/${id}_tmp
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_brain -in ${tdir}/${id}_tmp -init ${tdir}/${bsc}_pet2struc.mat -omat ${tdir}/${tf}_pet2struc.mat -out ${tdir}/${tf}_reg
fi
done
a=`for i in {0..3}; do printf " ${tdir}/${id}s%04d_reg " $i; done`
${FSLDIR}/bin/fslmerge -t ${wdir}/${id}_tmp_mvc $a
${FSLDIR}/bin/mcflirt -in ${wdir}/${id}_tmp_mvc -out ${wdir}/${id}_tmp_corr
${PIPEDIR}/bin/4dmean.pl ${wdir}/${id}_tmp_corr
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${wdir}/${id}_mean -omat ${wdir}/${id}_fbb2struc.mat -out ${wdir}/${id}_fbb
if [ $debug = 0 ] ; then
rm ${tdir}/${id}_tmp*
rm ${wdir}/${id}_tmp*
fi
4.- el mas complicado, usando una mascara. Este metodo se probo con el corregistro de PiBs y usa un umbral de intensidad
fbb_regm
- fbbtemp_regm.sh
#!/bin/sh
study=$1
shift
id=$1
shift
tdir=$1
shift
wdir=$1
shift
#sok=$1
#shift
treshold=$1
shift
debug=1
#Now get the uncorrected PETs and register to user space MRI
bsc=`printf "${id}s%04d" $sok`
${FSLDIR}/bin/fslreorient2std ${tdir}/${bsc} ${tdir}/${bsc}_tmp
if [ $treshold = 0 ] ; then
${FSLDIR}/bin/fslmaths ${tdir}/${bsc}_tmp -thr ${treshold} -bin ${tdir}/${bsc}_tmp_fbb_mask
else
${FSLDIR}/bin/fslmaths ${tdir}/${bsc}_tmp -thrP ${treshold} -bin ${tdir}/${bsc}_tmp_fbb_mask
fi
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${bsc}_tmp_fbb_mask -omat ${tdir}/${bsc}_tmp_fbb -dof 9
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${bsc} -applyxfm -init ${tdir}/${bsc}_tmp_fbb -out ${tdir}/${bsc}_reg -omat ${tdir}/${bsc}_pet2struc.mat
for i in {0..3}; do
if [ "$i" != "$sok" ]; then
tf=`printf "${id}s%04d" $i`
${FSLDIR}/bin/fslreorient2std ${tdir}/${tf} ${tdir}/${id}_tmp
if [ $treshold = 0 ] ; then
${FSLDIR}/bin/fslmaths ${tdir}/${id}_tmp -thr ${treshold} -bin ${tdir}/${tf}_tmp_fbb_mask
else
${FSLDIR}/bin/fslmaths ${tdir}/${id}_tmp -thrP ${treshold} -bin ${tdir}/${tf}_tmp_fbb_mask
fi
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${tf}_tmp_fbb_mask -omat ${tdir}/${tf}_tmp_fbb -init ${tdir}/${bsc}_pet2struc.mat -dof 9
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${tf} -applyxfm -init ${tdir}/${tf}_tmp_fbb -out ${tdir}/${tf}_reg
fi
done
a=`for i in {0..3}; do printf " ${tdir}/${id}s%04d_reg " $i; done`
${FSLDIR}/bin/fslmerge -t ${wdir}/${id}_tmp_mvc $a
${FSLDIR}/bin/mcflirt -in ${wdir}/${id}_tmp_mvc -out ${wdir}/${id}_tmp_corr
${PIPEDIR}/bin/4dmean.pl ${wdir}/${id}_tmp_corr
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${wdir}/${id}_mean -omat ${wdir}/${id}_fbb2struc.mat -out ${wdir}/${id}_fbb
if [ $debug = 0 ] ; then
rm ${tdir}/${id}_tmp*
rm ${wdir}/${id}_tmp*
fi
Esto lo he intentado agrupar en el script fbb_correct.pl,
fbb_correct.pl (chunk)
my $study;
my $cfile;
my $wbrain = 0;
my $wguide = 0;
my $wmask = 0;
my $sok = 0;
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
$_ = shift;
last if /^--$/;
if (/^-e/) { $study = shift; chomp($study);}
if (/^-cut/) { $cfile = shift; chomp($cfile);}
if (/^-useg/) { $sok = shift; $wguide = 1;}
if (/^-useb/) { $sok = shift; $wbrain = 1;}
if (/^-usem/) { $sok = shift; $wmask = 1;}
if (/^-h/) { print_help $ENV{'PIPEDIR'}.'/doc/fbb_reg.hlp'; exit;}
}
y despues,
foreach my $subject (@ok_pets){
$pm->start and next;
my $order;
if($wmask){
$order = "fbbtemp_regm.sh ".$study." ".$pets{$subject}.$subject." ".$petnc_dir." ".$w_dir." ".$sok;
}elsif($wguide){
$order = "fbbtemp_regc.sh ".$study." ".$pets{$subject}.$subject." ".$petnc_dir." ".$w_dir." ".$sok;
}elsif($wbrain){
$order = "fbbtemp_regb.sh ".$study." ".$pets{$subject}.$subject." ".$petnc_dir." ".$w_dir." ".$sok;
}else{
$order = "fbbtemp_reg.sh ".$study." ".$pets{$subject}.$subject." ".$petnc_dir." ".$w_dir;
}
print "$order\n";
system($order);
$pm->finish;
}
$pm->wait_all_children;
Resumiendo
si todo va bien basta con hacer:
$ fbb_correct.pl -e facehbi
$ parallel_fbb_rois_metrics.pl facehbi
Postprocessing
$ cd /home/osotolongo/Documents/ACE/facehbi
$ R CMD BATCH selected_mri.r
$ sed 's/"//g' facehbi_mri_selected.csv | awk -F"," '{if($1!="Subject") printf("%04d;%s;%s;%s;%s;%s;%s\n",$1,$2,$3,$4,$5,$6,$7); else printf("%s;%s;%s;%s;%s;%s;%s\n",$1,$2,$3,$4,$5,$6,$7)}' > facehbi_mri_selected_reformatted.csv
$ join -t";" -j 1 facehbi_fbb_fs_suvr_predef.csv facehbi_mri_selected_reformatted.csv > facehbi_fbb_mri.csv
$ sed 's/;/ /g' facehbi_fbb_mri.csv > facehbi_fbb_mri.dat
