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neuroimagen:vbm_ants

Plantilla y datos para VBM

Tengo muchos problemas para montar un VBM con las imagenes 3T, en particular con el protocolo BIOFACE. No soy capaz de registrarlas con FSL, asi que el FSLVBM no funciona. He intentado algun hack pero el registro es tan malo que no hay manera.

Así que me voy a montar un VBM a medida usando ANTs, que es lo que mejor me funciona para corregistro. Ver:

  1. https://github.com/asqwerty666/acevbm
  2. https://gsanroma.github.io/posts/2019/01/vbm-data-preparation/
  3. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLVBM/UserGuide#E_-_Obtaining_and_displaying_your_FSL-VBM_results

:ALERT: Merge: Custom VBM pipeline :ALERT:

get_fsaseg.sh
#!/bin/sh
 
fsid=$1
shift
 
id=$1
shift
 
dir=$1
shift
 
debug=0
 
#First get the freesurfer processed aseg.mgz
${FREESURFER_HOME}/bin/mri_label2vol --seg ${SUBJECTS_DIR}/${fsid}/mri/aseg.mgz --temp ${SUBJECTS_DIR}/${fsid}/mri/rawavg.mgz --o ${dir}/${id}_tmp_aseg.mgz --regheader ${SUBJECTS_DIR}/${fsid}/mri/aseg.mgz
${FREESURFER_HOME}/bin/mri_convert --in_type mgz --out_type nii ${dir}/${id}_tmp_aseg.mgz ${dir}/${id}_tmp_aseg.nii.gz
${FSLDIR}/bin/fslreorient2std ${dir}/${id}_tmp_aseg ${dir}/${id}_aseg
 
if [ $debug = 0 ] ; then
    rm ${dir}/${id}_tmp*
fi
get_lut.sh
#!/bin/sh
 
id=$1
shift
 
dir=$1
shift
 
lut=$1
shift
 
debug=0
 
${FSLDIR}/bin/fslmaths ${dir}/${id}_aseg.nii.gz -uthr ${lut} -thr ${lut} -div ${lut} ${dir}/${id}_${lut}.nii.gz
mktpl.pl
#!/usr/bin/perl
 
# Copyright 2021 O. Sotolongo <asqwerty@gmail.com>
 
use strict; use warnings;
use File::Temp qw(tempdir);
use File::Find::Rule;
use Cwd qw(getcwd);
use SLURM qw(send2slurm);
use File::Basename qw(basename);
use Data::Dump qw(dump);
my $odir;
my $ilist;
@ARGV = ("-h") unless @ARGV;
while (@ARGV and $ARGV[0] =~ /^-/) {
        $_ = shift;
        last if /^--$/;
        if (/^-o/) {$odir = shift; chomp $odir;}
        if (/^-i/) {$ilist = shift; chomp $ilist;}
}
 
die "Should supply output directory\n" unless $odir;
die "Should supply file list\n" unless $ilist;
 
my @gmluts = (3, 10, 11, 12, 13, 17, 18, 26, 42, 49, 50, 51, 52, 53, 54, 58);
my @wmluts = (2, 16, 28, 41, 60, 77, 85, 251, 252, 253, 254, 255);
my %subjects;
my $cwdir = getcwd();
my $wdir = $cwdir.'/working';
my $slurm_dir = $cwdir.'/slurm';
unless (-d $wdir) {mkdir $wdir;}
unless (-d $slurm_dir) {mkdir $slurm_dir;}
my %tplrun;
my %r_jobs;
$tplrun{'job_name'} = 'reg2tpl';
$tplrun{'cpus'} = 4;
$tplrun{'time'} = '4:0:0';
open IDF, "<$ilist" or die "Could not open file\n";
while (<IDF>) {
        my ($sid, $fsid) = /(.*),(.*)/;
        $subjects{$sid} = $fsid;
        my $tdir = tempdir( CLEANUP => 1);
        $tplrun{'filename'} = $slurm_dir.'/'.$sid.'_prepare2tpl.sh';
        $tplrun{'output'} = $slurm_dir.'/prep2tpl_output_'.$sid;
        $tplrun{'command'} = $ENV{'PIPEDIR'}.'/bin/get_fsaseg.sh '.$fsid.' '.$sid.' '.$tdir."\n";
        #my $order = $ENV{'PIPEDIR'}.'/bin/get_fsaseg.sh '.$fsid.' '.$sid.' '.$tdir;
        #system($order);
        my $imlist = $ENV{'FSLDIR'}.'/bin/fslmaths ';
        my $first = 1;
        foreach my $roi (@gmluts){
                $imlist .= ($first?' ':' -add ').$tdir.'/'.$sid.'_'.$roi.'.nii.gz';
                $first = 0;
                $tplrun{'command'} .= $ENV{'PIPEDIR'}.'/bin/get_lut.sh '.$sid.' '.$tdir.' '.$roi."\n";
                #$order = $ENV{'PIPEDIR'}.'/bin/get_lut.sh '.$sid.' '.$tdir.' '.$roi;
                #system($order);
        }
        $tplrun{'command'} .= $imlist.' '.$wdir.'/'.$sid.'_GM.nii.gz'."\n";
        #$order = $imlist.' '.$wdir.'/'.$sid.'_GM.nii.gz';
        #print "$order\n";
        #system($order);
        $imlist = $ENV{'FSLDIR'}.'/bin/fslmaths ';
        $first = 1;
        foreach my $roi (@wmluts){
                $imlist .= ($first?' ':' -add ').$tdir.'/'.$sid.'_'.$roi.'.nii.gz';
                $first = 0;
                $tplrun{'command'} .= $ENV{'PIPEDIR'}.'/bin/get_lut.sh '.$sid.' '.$tdir.' '.$roi."\n";
                #$order = $ENV{'PIPEDIR'}.'/bin/get_lut.sh '.$sid.' '.$tdir.' '.$roi;
                #system($order);
        }
        $tplrun{'command'} .= $imlist.' '.$wdir.'/'.$sid.'_WM.nii.gz'."\n";
        #$order = $imlist.' '.$wdir.'/'.$sid.'_WM.nii.gz';
        #system($order);
        my $job_id = send2slurm(\%tplrun);
        $r_jobs{$sid} = $job_id;
}
close IDF;
my $tmp = tempdir( CLEANUP => 1);
my @twm; my @tgm;
my @t_jobs;
my $toprint = '';;
my $seg_file = 'seg_files.csv';
my $flist = $wdir.'/'.$seg_file;
open TPF,">$flist" or die "$!\n";
foreach my $sid (sort keys %subjects){
        $tplrun{'filename'} = $slurm_dir.'/'.$sid.'_prepare2tpl.sh';
        $tplrun{'output'} = $slurm_dir.'/prep2tpl_output_'.$sid;
        $tplrun{'dependency'} = 'afterok:'.$r_jobs{$sid};
        $tplrun{'command'} = $ENV{'ANTS_PATH'}.'/antsRegistrationSyNQuick.sh -d 3 -f '.$ENV{'FSLDIR'}.'/data/standard/MNI152_T1_2mm.nii.gz -m '.$wdir.'/'.$sid.'_GM.nii.gz -t a -o '.$tmp.'/'.$sid.'_GM_init_'."\n";
        #system($order);
        $tplrun{'command'} .= $ENV{'ANTS_PATH'}.'/antsApplyTransforms -d 3 -r '.$ENV{'FSLDIR'}.'/data/standard/MNI152_T1_2mm.nii.gz -i '.$wdir.'/'.$sid.'_GM.nii.gz -t '.$tmp.'/'.$sid.'_GM_init_0GenericAffine.mat -o '.$tmp.'/'.$sid.'_GM0.nii.gz'."\n";
        #system($order);
        push @tgm, $tmp.'/'.$sid.'_GM0.nii.gz';
        $tplrun{'command'} .= $ENV{'ANTS_PATH'}.'/antsRegistrationSyNQuick.sh -d 3 -f '.$ENV{'FSLDIR'}.'/data/standard/MNI152_T1_2mm.nii.gz -m '.$wdir.'/'.$sid.'_WM.nii.gz -t a -o '.$tmp.'/'.$sid.'_WM_init_'."\n";
        #system($order);
        $tplrun{'command'} .= $ENV{'ANTS_PATH'}.'/antsApplyTransforms -d 3 -r '.$ENV{'FSLDIR'}.'/data/standard/MNI152_T1_2mm.nii.gz -i '.$wdir.'/'.$sid.'_WM.nii.gz -t '.$tmp.'/'.$sid.'_WM_init_0GenericAffine.mat -o '.$tmp.'/'.$sid.'_WM0.nii.gz'."\n";
        #system($order);
        push @twm, $tmp.'/'.$sid.'_WM0.nii.gz';
        $toprint .= $wdir.'/'.$sid.'_GM.nii.gz,'.$wdir.'/'.$sid.'_WM.nii.gz'."\n";
        my $job_id = send2slurm(\%tplrun);
        push @t_jobs, $job_id;
 
}
my %tplmk;
$tplmk{'job_name'} = 'merge_all';
$tplmk{'cpus'} = 4;
$tplmk{'time'} = '4:0:0';
$tplmk{'dependency'} = 'afterok:'.join(',',@t_jobs);
$tplmk{'output'} = $slurm_dir.'/merge2tpl_output';
$tplmk{'filename'} = $slurm_dir.'/merge2tpl.sh';
my $aux = join ' ',@tgm;
$tplmk{'command'} = $ENV{'FSLDIR'}.'/bin/fslmerge -t '.$tmp.'/GM0template.nii.gz '.$aux."\n";
#system($order);
$tplmk{'command'} .= $ENV{'FSLDIR'}.'/bin/fslmaths '.$tmp.'/GM0template.nii.gz '.$tmp.'/avg_GM.nii.gz'."\n";
#system($order);
$aux = join ' ',@twm;
$tplmk{'command'} .= $ENV{'FSLDIR'}.'/bin/fslmerge -t '.$tmp.'/WM0template.nii.gz '.$aux."\n";
#system($order);
$tplmk{'command'} .= $ENV{'FSLDIR'}.'/bin/fslmaths '.$tmp.'/WM0template.nii.gz '.$tmp.'/avg_WM.nii.gz';
#system($order);
my $mjob = send2slurm(\%tplmk);
open TPF,">$flist" or die "$!\n";
        print TPF $toprint;
close TPF;
my $order = $ENV{'ANTS_PATH'}.'/waitForSlurmJobs.pl 0 600 '.$mjob;
system($order);
 
$order = 'cd '.$wdir.';'.$ENV{'ANTS_PATH'}.'/antsMultivariateTemplateConstruction2.sh -d 3 -a 0 -b 0 -c 5 -u 1:0:0 -e 1 -g 0.25 -i 4 -k 2 -w 1x1 -q 70x50x30x10 -f 6x4x2x1 -s 3x2x1x0 -n 0 -o antsTPL_ -r 0 -l 1 -m CC -t SyN -y 0 -z '.$tmp.'/avg_GM.nii.gz -z '.$tmp.'/avg_WM.nii.gz '.$seg_file;
print "$order\n";
system($order);
foreach my $sid (sort keys %subjects){
        my $order = $ENV{'ANTS_PATH'}.'/antsApplyTransforms -d 3 -i '.$wdir.'/'.$sid.'_GM.nii.gz -r '.$wdir.'/antsTPL_template0.nii.gz -o '.$wdir.'/'.$sid.'_fulltransf.nii.gz -t '.$wdir.'/antsTPL_'.$sid.'_GM*1Warp.nii.gz -t '.$wdir.'/antsTPL_'.$sid.'_GM*0GenericAffine.mat --float || true';
        print "$order\n";
        system($order);
        $order = $ENV{'ANTS_PATH'}.'/CreateJacobianDeterminantImage 3 '.$wdir.'/'.$sid.'_fulltransf.nii.gz '.$wdir.'/'.$sid.'_jacobian.nii.gz 0 1 || true';
        print "$order\n";
        system($order);
        $order = $ENV{'FSLDIR'}.'/bin/fslmaths '.$wdir.'/'.$sid.'_fulltransf.nii.gz -mul '.$wdir.'/'.$sid.'_jacobian.nii.gz '.$wdir.'/'.$sid.'_GM2temp_mod';
        print "$order\n";
        system($order);
}
my @regoks = find(file => 'name' => "*_fulltransf.nii.gz", in => $wdir);
@regoks = sort @regoks;
my @fsums;
my $nomodsums = join ' ', @regoks;
(my $modsums = $nomodsums) =~ s/fulltransf/GM2temp_mod/g;
my $statsdir = $cwdir.'/stats';
unless (-d $statsdir) {mkdir $statsdir;}
$order = $ENV{'FSLDIR'}.'/bin/fslmerge -t '.$statsdir.'/GM_merg '.$nomodsums;
print "$order\n";
system($order);
$order = $ENV{'FSLDIR'}.'/bin/fslmerge -t '.$statsdir.'/GM_mod_merg '.$modsums;
print "$order\n";
system($order);
open ROF,">niceregister.list";
foreach my $regok (@regoks){
        $regok = basename $regok;
        $regok =~ s/(.*)_.*/$1/;
        print ROF "$regok\n";
}
close ROF;
neuroimagen/vbm_ants.txt · Last modified: 2021/05/05 09:21 by osotolongo