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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. 
* Pagina vieja * 
$ dcm2nii -o tmp/ /nas/raw_images/facehbi/fbb/FACEHBI-F023B/DICOM/15020608/57070000/57437982
y podemos tener las sigientes situaciones:
Esto es lo ideal y se convierte facilmente en 4 archivos distintos
$ fslsplit s005a2001.nii.gz ../fbb_first/smc0023s -t
Lo peor no es que esten apiladas mal sino que el numero de slices de cada imagen es bastante arbitrario. Hay que abrir la imagen y seleccionarlos manualmente
$ ls -lh
total 70M
-rw-rw-r-- 1 osotolongo osotolongo 16M Mar 6 2015 s004a2001.nii.gz
-rw-rw-r-- 1 osotolongo osotolongo 54M Mar 6 2015 s005a2001.nii.gz
$ fslview s005a2001.nii.gz &
$ mkdir splitted; fslsplit s005a2001.nii.gz splitted/s004a -z
$ a=`for i in {0..85}; do printf "splitted/s004a%04d " $i; done`; fslmerge -z ../fbb_first/smc0021s0000 $a
$ a=`for i in {85..185}; do printf "splitted/s004a%04d " $i; done`; fslmerge -z ../fbb_first/smc0021s0001 $a
$ a=`for i in {185..280}; do printf "splitted/s004a%04d " $i; done`; fslmerge -z ../fbb_first/smc0021s0002 $a
$ a=`for i in {280..390}; do printf "splitted/s004a%04d " $i; done`; fslmerge -z ../fbb_first/smc0021s0003 $a
$ rm -rf *
Esto es lo peor, y creo que lo hacen para joder, pero la solucion es combinar los dos metodos anteriores
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;
