Update 'datacite.yml'

datacite.yml

@@ -1,458 +1,43 @@
-Accurate non-linear registration of cortical and subcortical labelling from Mindboggle 101 to the symmetric MNI-ICBM2009c atlas followed by manual editing.
+authors:
+  -
+    firstname: "Ana"
+    lastname: "Manera"
+    affiliation: "McGill University"
+    id: "ORCID:0000-0003-1639-6858"
+  -
+    firstname: "Mahsa"
+    lastname: "Dadar"
+    affiliation: "McGill University"
+    id: "ORCID:0000-0003-4008-2672"
+  -
+    firstname: "Vladimir"
+    lastname: "Fonov"
+    affiliation: "McGill University"
+  -
+    firstname: "D. Louis"
+    lastname: "Collins"
+    affiliation: "McGill University"
 
-ants_nl_registration.sh
+title: "CerebrA: Accurate registration and manual label correction of the Mindboggle-101 atlas for the MNI-ICBM152 template"
 
-#! /bin/bash
+description: |
+The present repository contains the Cerebrum Atlas (CerebrA) along with the MNI-ICBM2009c average template. 
+MNI-ICBM2009c is the most recent version of the MNI-ICBM152 brain average with more anatomical details. 
+Cerebra is based on an accurate non-linear registration of cortical and subcortical labelling from Mindboggle 101
+to the symmetric MNI-ICBM2009c atlas, followed by manual editing. 
 
-if [ $# -eq 3 ];then
-    src=$1
-    trg=$2
-    outp=$3
-elif [ $# -eq 5 ];then
-    src=$1
-    trg=$2
-    src_mask=$3
-    trg_mask=$4
-    outp=$5
-else
- echo "Usage $0 <source> <target> [source mask] [target mask] <output_prefix>"
- echo "Output will be <output_prefix>0_NL.xfm and <output_prefix>0NL_inverse.xfm with corresponding grid files"
- exit 1
-fi
 
-if [ ! -z $trg_mask ];then
-mask="-x [${src_mask},${trg_mask}] "
-fi
+keywords:
+  - Atlas
+  - Average template
+  - Magnetic resonance imaging
 
 
-antsRegistration -v -d 3 --float 1 \
-    --output "[${outp}]" \
-    --use-histogram-matching 0 --winsorize-image-intensities "[0.005,0.995]" \
-    --transform "SyN[0.7,3,0]" \
-        --metric "CC[${src},${trg},1,4]" \
-        --convergence "[50x50x30,1e-6,10]" \
-        --shrink-factors 4x2x1 --smoothing-sigmas 2x1x0vox \
-        ${mask} --minc
-bestlinreg_s2
+license:
+  name: "Creative Commons CC0 1.0 Universal"
+  url: "https://creativecommons.org/publicdomain/zero/1.0/"
 
-#! /usr/bin/env perl
-#
-# linear fitting using parameters optimised by Claude Lepage,
-# using a brain mask for the source and the target. This was
-# greatly inspired by best1stepnlreg.pl by Steve Robbins.
-#
-# Claude Lepage - claude@bic.mni.mcgill.ca
-# Andrew Janke - rotor@cmr.uq.edu.au
-# Center for Magnetic Resonance
-# The University of Queensland
-# http://www.cmr.uq.edu.au/~rotor
-#
-# Copyright Andrew Janke, The University of Queensland.
-# Permission to use, copy, modify, and distribute this software and its
-# documentation for any purpose and without fee is hereby granted,
-# provided that the above copyright notice appear in all copies.  The
-# author and the University of Queensland make no representations about the
-# suitability of this software for any purpose.  It is provided "as is"
-# without express or implied warranty.
 
-use strict;
-use warnings "all";
-use Getopt::Tabular;
-use File::Basename;
-use File::Temp qw/ tempdir /;
+resourcetype: Dataset
 
-my @conf = (
 
-   { type        => "blur",
-     trans       => [qw/-est_translations/],
-     blur_fwhm   => 16,
-     steps       => [qw/8 8 8/],
-     tolerance   => 0.01,
-     simplex     => 32 },
-
-   { type        => "blur",
-     trans       => undef,
-     blur_fwhm   => 8,
-     steps       => [qw/4 4 4/],
-     tolerance   => 0.004,
-     simplex     => 16 },
-
-   { type        => "blur",
-     trans       => undef,
-     blur_fwhm   => 4,
-     steps       => [qw/4 4 4/],
-     tolerance   => 0.004,
-     simplex     => 8 },
-
-   { type        => "dxyz",
-     trans       => undef,
-     blur_fwhm   => 8,
-     steps       => [qw/4 4 4/],
-     tolerance   => 0.004,
-     simplex     => 4 },
-
-   { type        => "dxyz",
-     trans       => undef,
-     blur_fwhm   => 4,
-     steps       => [qw/4 4 4/],
-     tolerance   => 0.004,
-     simplex     => 2 }
-     
-   );
-
-
-my($Help, $Usage, $me);
-my(@opt_table, %opt, $source, $target, $outxfm, $outfile, @args, $tmpdir);
-
-$me = &basename($0);
-%opt = (
-   'verbose'   => 1,
-   'clobber'   => 0,
-   'fake'      => 0,
-   'init_xfm'  => undef,
-   'source_mask' => undef,
-   'target_mask' => undef,
-   'lsqtype'     => "-lsq9",
-   'work_dir'    => undef,
-   'sec_source'  => undef,
-   'sec_target'  => undef,
-   'cost_function' => '-xcorr',
-   'noshear'     => 0,
-   'noscale'     => 0,
-   'norot'       => 0,
-   'noshift'     => 0,
-   'close'       => 0,
-   );
-
-$Help = <<HELP;
-| $me does hierachial linear fitting between two files.
-|    you will have to edit the script itself to modify the
-|    fitting levels themselves
-| 
-| Problems or comments should be sent to: claude\@bic.mni.mcgill.ca
-HELP
-
-$Usage = "Usage: $me [options] source.mnc target.mnc output.xfm [output.mnc]\n".
-         "       $me -help to list options\n\n";
-
-@opt_table = (
-   ["-verbose", "boolean", 0, \$opt{verbose},
-      "be verbose" ],
-   ["-clobber", "boolean", 0, \$opt{clobber},
-      "clobber existing check files" ],
-   ["-fake", "boolean", 0, \$opt{fake},
-      "do a dry run, (echo cmds only)" ],
-   ["-init_xfm", "string", 1, \$opt{init_xfm},
-      "initial transformation (default identity)" ],
-   ["-source_mask", "string", 1, \$opt{source_mask},
-      "source mask to use during fitting" ],
-   ["-target_mask", "string", 1, \$opt{target_mask},
-      "target mask to use during fitting" ],
-   ["-lsq9", "const", "-lsq9", \$opt{lsqtype},
-      "use 9-parameter transformation (default)" ],
-   ["-lsq12", "const", "-lsq12", \$opt{lsqtype},
-      "use 12-parameter transformation (default -lsq9)" ],
-   ["-lsq6", "const", "-lsq6", \$opt{lsqtype},
-      "use 6-parameter transformation" ],
-   ["-lsq7", "const", "-lsq7", \$opt{lsqtype},
-      "use 7-parameter transformation" ],
-   ["-quaternions","const",'-quaternions', \$opt{lsqtype},
-      "use quaternion transformation" ],
-   ["-mi","const",'-mi', \$opt{cost_function},
-      "Mutual information cost function" ],
-   ["-xcorr","const",'-xcorr', \$opt{cost_function},
-      "Cross-correlation cost function" ],
-   ["-work_dir", "string", 1, \$opt{work_dir},
-      "Directory to keep blurred files" ],
-   ["-sec_source", "string", 1, \$opt{sec_source},
-      "secondaty source" ],
-   ["-sec_target", "string", 1, \$opt{sec_target},
-      "secondary target" ],
-   ["-noshear", "boolean", 1, \$opt{noshear},
-      "lsq12 w/o shear" ],
-   ["-noscale", "boolean", 1, \$opt{noscale},
-      "lsq12 w/o scale" ],
-   ["-norot", "boolean", 1, \$opt{norot},
-      "lsq12 w/o rotations" ],
-   ["-noshift", "boolean", 1, \$opt{noshift},
-      "lsq12 w/o shifts" ],
-   ["-close", "boolean", 1, \$opt{close},
-      "Samples are close" ],
-   );
-
-delete $ENV{MINC_COMPRESS} if $ENV{MINC_COMPRESS};
-
-# Check arguments
-&Getopt::Tabular::SetHelp($Help, $Usage);
-&GetOptions (\@opt_table, \@ARGV) || exit 1;
-die $Usage if(! ($#ARGV == 2 || $#ARGV == 3));
-$source = shift(@ARGV);
-$target = shift(@ARGV);
-$outxfm = shift(@ARGV);
-$outfile = (defined($ARGV[0])) ? shift(@ARGV) : undef;
-
-# check for files
-die "$me: Couldn't find input file: $source\n\n" if (!-e $source);
-die "$me: Couldn't find input file: $target\n\n" if (!-e $target);
-if(-e $outxfm && !$opt{clobber}){
-   die "$me: $outxfm exists, -clobber to overwrite\n\n";
-   }
-if(defined($outfile) && -e $outfile && !$opt{clobber}){
-   die "$me: $outfile exists, -clobber to overwrite\n\n";
-   }
-
-# make tmpdir
-$tmpdir = &tempdir( "$me-XXXXXXXX", TMPDIR => 1, CLEANUP => 1 );
-$opt{work_dir}=$tmpdir unless $opt{work_dir};
-
-# set up filename base
-my($i, $s_base, $t_base, $tmp_xfm, $tmp_source, $tmp_target, $prev_xfm,
-$tmp_sec_source, $tmp_sec_target);
-
-$s_base = &basename($source);
-$s_base =~ s/\.mnc(.gz)?$//;
-$s_base = 's_'.$s_base;
-
-$t_base = &basename($target);
-$t_base =~ s/\.mnc(.gz)?$//;
-$t_base = 't_'.$t_base;
-
-# Mask the source and target once before blurring. Both masks must exist.
-
-my $source_masked = $source;
-my $target_masked = $target;
-
-# initial transformation supplied by the user, applied to both the 
-# source image and its mask.
-
-#if( defined $opt{init_xfm} ) { 
-#  my $source_resampled = "${tmpdir}/${s_base}_resampled.mnc";
-#  &do_cmd( 'mincresample', 
-#           '-clobber', 
-#           '-like', $target_masked, 
-#           '-transform', $opt{init_xfm}, 
-#           $source_masked, $source_resampled );
-#  $source_masked = $source_resampled;
-
-#  #apply it to the mask, if it's defined
-#  if(defined($opt{source_mask}))
-#  {
-#    my $mask_resampled = "${tmpdir}/${s_base}_mask_resampled.mnc";
-#    &do_cmd( 'mincresample', '-clobber', '-like', $target_masked,
-#             '-nearest_neighbour', '-transform', $opt{init_xfm}, 
-#             $opt{source_mask}, $mask_resampled );
-#    $opt{source_mask} = $mask_resampled;
-#  }
-#}
-
-$prev_xfm = undef;
-
-# a fitting we shall go...
-for ($i=0; $i<=$#conf; $i++){
-   
-   # set up intermediate files
-   $tmp_xfm = "$tmpdir/$s_base\_$i.xfm";
-   $tmp_source = "$opt{work_dir}/$s_base\_$conf[$i]{blur_fwhm}";
-   $tmp_target = "$opt{work_dir}/$t_base\_$conf[$i]{blur_fwhm}";
-
-   $tmp_source = "$opt{work_dir}/$s_base\_$conf[$i]{blur_fwhm}";
-   $tmp_target = "$opt{work_dir}/$t_base\_$conf[$i]{blur_fwhm}";
-    
-   if($opt{close})
-   {
-     next if($conf[$i]{blur_fwhm}>8);
-     $conf[$i]{simplex}=1;
-     $conf[$i]{steps}=[qw/2 2 2/];
-   }
-
-   print STDOUT "-+-------------------------[$i]-------------------------\n".
-                " | steps:          @{$conf[$i]{steps}}\n".
-                " | blur_fwhm:      $conf[$i]{blur_fwhm}\n".
-                " | simplex:        $conf[$i]{simplex}\n".
-                " | source:         $tmp_source\_$conf[$i]{type}.mnc\n".
-                " | target:         $tmp_target\_$conf[$i]{type}.mnc\n".
-                " | xfm:            $tmp_xfm\n".
-                "-+-----------------------------------------------------\n".
-                "\n";
-   
-   # blur the masked source and target images
-   my @grad_opt = ();
-   push( @grad_opt, '-gradient' ) if( $conf[$i]{type} eq "dxyz" );
-   
-   if($conf[$i]{blur_fwhm}>0) # actually this should be 1
-   {
-     if(!-e "$tmp_source\_$conf[$i]{type}.mnc") {
-       &do_cmd('mincblur', '-clobber', '-no_apodize', '-fwhm', $conf[$i]{blur_fwhm},
-               @grad_opt, $source_masked, $tmp_source);
-     }
-     if(!-e "$tmp_target\_$conf[$i]{type}.mnc") {
-       &do_cmd('mincblur', '-clobber', '-no_apodize', '-fwhm', $conf[$i]{blur_fwhm},
-               @grad_opt, $target_masked, $tmp_target);
-     }
-     if(defined($opt{sec_source}) && defined($opt{sec_target}) )
-     {
-       $tmp_sec_source = "$opt{work_dir}/sec_$s_base\_$conf[$i]{blur_fwhm}";
-       $tmp_sec_target = "$opt{work_dir}/sec_$t_base\_$conf[$i]{blur_fwhm}";
-       if(! -e "$tmp_sec_source\_$conf[$i]{type}.mnc")
-       {
-        &do_cmd('mincblur', '-clobber', '-no_apodize', '-fwhm',
-               $conf[$i]{blur_fwhm},
-               @grad_opt, $opt{sec_source}, $tmp_sec_source);
-       }
-
-       if(! -e "$tmp_sec_target\_$conf[$i]{type}.mnc")
-       {
-        &do_cmd('mincblur', '-clobber', '-no_apodize', '-fwhm',
-               $conf[$i]{blur_fwhm},
-               @grad_opt, $opt{sec_target}, $tmp_sec_target);
-       }
-       $tmp_sec_source="$tmp_sec_source\_$conf[$i]{type}.mnc";
-       $tmp_sec_target="$tmp_sec_target\_$conf[$i]{type}.mnc";
-     }
-   } else { # noop
-     if(!-e "$tmp_source\_$conf[$i]{type}.mnc") {
-       do_cmd('ln','-s',$source_masked,"$tmp_source\_$conf[$i]{type}.mnc");
-     }
-     if(!-e "$tmp_target\_$conf[$i]{type}.mnc") {
-       &do_cmd('ln', '-s', $target_masked, "$tmp_target\_$conf[$i]{type}.mnc");
-     }
-     if(defined($opt{sec_source}) && defined($opt{sec_target}) )
-     {
-       $tmp_sec_source =$opt{sec_source};
-       $tmp_sec_target =$opt{sec_target};
-     }
-   }
-   # set up registration
-   @args = ('minctracc', '-clobber', $opt{lsqtype},
-            '-step', @{$conf[$i]{steps}}, '-simplex', $conf[$i]{simplex},
-            '-tol', $conf[$i]{tolerance});
-
-   # Initial transformation will be computed from the from Principal axis 
-   # transformation (PAT).
-   push(@args, @{$conf[$i]{trans}}) if( defined $conf[$i]{trans} && !$opt{init_xfm} );
-
-   # Current transformation at this step
-   if( defined $prev_xfm ) 
-   {
-     push(@args, '-transformation', $prev_xfm ) ;
-   } elsif( defined $opt{init_xfm} ) { 
-     push(@args, '-transformation', $opt{init_xfm} ) ;
-     #push(@args, '-est_center' ) ;
-     
-   } elsif($opt{close}) {
-    push(@args, '-identity') ;  
-   }
-
-   # masks (even if the blurred image is masked, it's still preferable
-   # to use the mask in minctracc)
-   push(@args, '-source_mask', $opt{source_mask} ) if defined($opt{source_mask});
-   push(@args, '-model_mask', $opt{target_mask}) if defined($opt{target_mask});
-
-   if($tmp_sec_source && $tmp_sec_target )
-   {
-     push(@args, $opt{cost_function},
-       "$tmp_source\_$conf[$i]{type}.mnc",
-       "$tmp_target\_$conf[$i]{type}.mnc");
-     push(@args, '-feature_vol',$tmp_sec_source,$tmp_sec_target,'xcorr',1.0);
-   } else {
-     push(@args, $opt{cost_function},"$tmp_source\_$conf[$i]{type}.mnc",
-                 "$tmp_target\_$conf[$i]{type}.mnc");
-   }
-
-   push @args,'-w_shear',0,0,0 if $opt{noshear};
-   push @args,'-w_scales',0,0,0 if $opt{noscale};
-   push @args,'-w_translations',0,0,0 if $opt{noshift};
-   push @args,'-w_rotations',0,0,0 if $opt{norot};
-   
-   # add files and run registration
-   push(@args, $tmp_xfm);
-   &do_cmd(@args);
-   
-   $prev_xfm = $tmp_xfm;
-}
-
-# Concatenate transformations if an initial transformation was given.
-
-#if( defined $opt{init_xfm} ) { 
-#  &do_cmd( 'xfmconcat', $prev_xfm, $opt{init_xfm}, $outxfm );
-#} else {
-  do_cmd( 'mv', '-f', $prev_xfm, $outxfm );
-#}
-
-# resample if required
-if(defined($outfile)){
-   print STDOUT "-+- creating $outfile using $outxfm\n".
-   &do_cmd( 'mincresample', '-clobber', '-like', $target,
-            '-transformation', $outxfm, $source, $outfile );
-}
-
-sub do_cmd { 
-   print STDOUT "@_\n" if $opt{verbose};
-   if(!$opt{fake}){
-      system(@_) == 0 or die;
-   }
-}
-
-linear_registration.sh
-
-bestlinreg_s2 DKT_Atlas.mnc mni_icbm152_t1_tal_nlin_sym_09c.mnc  DKT2icbm.xfm --lsq9
-
-resampling.sh
-
-itk_resample DKT_Atlas.mnc --like mni_icbm152_t1_tal_nlin_sym_09c.mnc --transform DKT2icbmnl.xfm DKT_Atlas_icbm_nl.mnc --label --clobber
-
-CerebrA_LabelDetails.csv 
-
-Mindboggle ID,Label Name,CerebrA ID,,Notes,Dice Kappa
-,,RH Labels,LH Labels,,
-2002,Caudal Anterior Cingulate,30,81,,0.79
-2003,Caudal Middle Frontal,42,93,Improved distinction from Precentral ,0.73
-2005,Cuneus,43,94,,0.67
-2006,Entorhinal,36,87,Improved delimitation ,0.78
-2007,Fusiform,24,75,,0.77
-2008,Inferior Parietal,10,61,,0.75
-2009,Inferior temporal,3,54,Removed dorsal part MT,0.72
-2010,Isthmus Cingulate,33,84,,0.79
-2011,Lateral Occipital,34,85,,0.76
-2012,Lateral Orbitofrontal,7,58,,0.8
-2013,Lingual,12,63,,0.75
-2014,Medial Orbitofrontal,15,66,,0.72
-2015,Middle Temporal,28,79,Added dorsal part,0.72
-2016,Parahippocampal,18,69,,0.86
-2017,Paracentral,16,67,,0.77
-2018,Pars Opercularis,32,83,,0.77
-2019,Pars Orbitalis,44,95,,0.8
-2020,Pars Triangularis,22,73,,0.76
-2021,Pericalcarine,6,57,,0.6
-2022,Postcentral,13,64,,0.82
-2023,Posterior Cingulate,47,98,,0.8
-2024,Precentral,35,86,,0.84
-2025,Precuneus,31,82,,0.8
-2026,Rostral Anterior Cingulate,8,59,,0.72
-2027,Rostral Middle Frontal,1,52,Improved delimitation from CMF,0.74
-2028,Superior Frontal,38,89,,0.82
-2029,Superior Parietal,9,60,Improved delimitation from Precuneus and IP,0.72
-2030,Superior Temporal,45,96,Added dorsal part limiting with IP and Supramarginal,0.87
-2031,Supramarginal,51,102,,0.81
-2034,Transverse Temporal,14,65,,0.85
-2035,Insula,23,74,,0.88
-16,Brainstem,11,62,"Completed filling, removed labelled voxels out of actual brainstem and removed CWM labels in brainstem area. ",0.65
-14,Third Ventricle,29,80,,0.68
-15,Fourth Ventricle,37,88,Missing label. Manually delimited using CSF threshold.  ,0.39
-85,Optic Chiasm,17,68,Almost inexistent label and out of place in original labelling  Completed OC and tracts (originally labelled as Ventral Diencephalon),0
-43,Lateral Ventricle,41,92,Improved continuity of labelled voxels,0.89
-44,Inferior Lateral Ventricle,5,56,,0.12
-45,Cerebellum Gray Matter,46,97,"Completed filling using threshold for CGM, removed cerebellum labels out of area (within brainstem and vermis area)",0.83
-46,Cerebellum White Matter,39,90,"Improved according threshold for CWM, removed labels in brainstem and vermis. ",0.73
-49,Thalamus,40,91,,0.97
-50,Caudate,49,100,Completed filling using threshold ,0.84
-51,Putamen,21,72,Corrected uniformity using threshold,0.87
-52,Pallidum,27,78,Improved delimitation between putamen and pallidum,0.83
-53,Hippocampus,48,99,,0.69
-54,Amygdala,19,70,,0.64
-58,Accumbens Area,4,55,,0.76
-60,Ventral Diencephalon,26,77,,0.93
-92,Basal Forebrain,25,76,,0.82
-630,Vermal lobules I-V,50,101,Improved delimitation with other vermal lobules and cerebellar hemispheres,0.66
-631,Vermal lobules VI-VII,2,53,Improved delimitation with other vermal lobules and cerebellar hemispheres,0.38
-632,Vermal lobules VIII-X,20,71,Improved delimitation with other vermal lobules and cerebellar hemispheres,0.44