neuroimagen:vbm_ants
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Plantilla y datos para VBM
Tengo muchos problemas para montar un VBM con
- 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.1620205414.txt.gz · Last modified: 2021/05/05 09:03 by osotolongo
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