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Added version tracking for dynamic atlases
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Bogdan Petre committed Nov 3, 2023
1 parent 29257ab commit 4f6b6e4
Showing 1 changed file with 84 additions and 65 deletions.
149 changes: 84 additions & 65 deletions CanlabCore/Data_extraction/load_atlas.m
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% List of keywords/atlases available:
% -------------------------------------------------------------------------
% 'canlab2023[_fine|_coarse][_fmriprep20|_fsl6][_2mm]
% 'Combined atlas from other published atlases, whole brain. Available in a fine or coarse (default) parcellation
% in MNI152NLin2009cAsym (aka fmriprep) space (default) or MNI152NLin6Asym (aka fsl) space in 1mm or 2mm (default)
% resolutions. Note atlases are best if thresholded using atlas/threshold to p>0.2. Refer to github README for
% more details.'
% 'Combined atlas from other published, whole brain. Available in a fine or coarse (default) parcellation in
% MNI152NLin2009cAsym (aka fmriprep) space (default) or MNI152NLin6Asym (aka fsl) space in 1mm or 2mm (default)
% resolutions. Refer to github README for details.'
% 'canlab2018[_2mm]' 'Combined atlas from other published atlases, whole brain. (Deprecated in favor of canlab2023)'
% 'thalamus' 'Thalamus_combined_atlas_object.mat'
% 'thalamus_detail', 'morel[_fsl6|_fmriprep20]',
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docustom = 0;
verbose = 1;
docreate = 0;

% optional inputs with default values
% -----------------------------------
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switch lower(atlas_file_name_or_keyword)

case {'thalamus'}
case {'thalamus', 'morel'}
warning('This atlas is deprecated. Please specify thalamus_[fsl6|fmriprep20] instead.');
savefile = which('Thalamus_combined_atlas_object.mat');
varname = 'thalamus_atlas';

case {'thalamus_detail', 'morel', 'morel_fsl6'}
case {'thalamus_detail', 'morel_fsl6'}
savefile = which('Morel_thalamus_atlas_object.mat');
varname = 'atlas_obj';

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varname = 'atlas_obj';

case {'bianciardi', 'bianciardi_coarse', 'bianciardi_fmriprep20', 'bianciardi_coarse_fmriprep20'}
savefile='bianciardi_fmriprep20_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin2009cAsym',false);
end
savefile='bianciardi_coarse_MNI152NLin2009cAsym_atlas_object.mat';
varname = 'bianciaAtlas';
docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin2009cAsym',false);

case {'bianciardi_fine', 'bianciardi_fine_fmriprep20'}
savefile='bianciardi_fmriprep20_fine_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin2009cAsym',true);
end
savefile='bianciardi_fine_MNI152NLin2009cAsym_atlas_object.mat';
varname = 'bianciaAtlas';
docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin2009cAsym',true);

case {'bianciardi_fsl6', 'bianciardi_coarse_fsl6'}
savefile='bianciardi_fsl6_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin6Asym',false);
end
savefile='bianciardi_coarse_MNI152NLin6Asym_atlas_object.mat';
varname = 'bianciaAtlas';
docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin6Asym',false);

case {'bianciardi_fine_fsl6'}
savefile='bianciardi_fsl6_fine_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin6Asym',true);
end
savefile='bianciardi_fine_MNI152NLin6Asym_atlas_object.mat';
varname = 'bianciaAtlas';
docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin6Asym',true);

case {'bianciardi_2mm', 'bianciardi_coarse_2mm', 'bianciardi_fmriprep20_2mm', 'bianciardi_coarse_fmriprep20_2mm'}
savefile='bianciardi_fmriprep20_2mm_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin2009cAsym_2mm',false);
end
savefile='bianciardi_coarse_MNI152NLin2009cAsym_2mm_atlas_object.mat';
varname = 'bianciaAtlas';
docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin2009cAsym_2mm',false);

case {'bianciardi_fine_2mm', 'bianciardi_fine_fmriprep20_2mm'}
savefile='bianciardi_fmriprep20_2mm_fine_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin2009cAsym_2mm',true);
end
savefile='bianciardi_fine_MNI152NLin2009cAsym_2mm_atlas_object.mat';
varname = 'bianciaAtlas';
docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin2009cAsym_2mm',true);

case {'bianciardi_fsl6_2mm', 'bianciardi_coarse_fsl6_2mm'}
savefile='bianciardi_fsl6_2mm_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin6Asym_2mm',false);
end
savefile='bianciardi_coarse_MNI152NLin6Asym_2mm_atlas_object.mat';
varname = 'bianciaAtlas';
docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin6Asym_2mm',false);

case {'bianciardi_fine_fsl6_2mm'}
savefile='bianciardi_fsl6_2mm_fine_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('bianciardi_create_atlas_obj.m')))
bianciardi_create_atlas_obj('MNI152NLin6Asym_2mm',true);
end
savefile='bianciardi_fine_MNI152NLin6Asym_2mm_atlas_object.mat';
varname = 'bianciaAtlas';

docreate = true;
create_atlas = @(x1)bianciardi_create_atlas_obj('MNI152NLin6Asym_2mm',true);

case {'canlab2023_coarse_fmriprep20_2mm', 'canlab2023_coarse_fmriprep20','canlab2023_coarse_2mm', ...
'canlab2023_fmriprep20_2mm', 'canlab2023_coarse', 'canlab2023_fmriprep20', 'canlab2023_2mm', ...
'canlab2023'}
savefile='CANLab2023_coarse_fmriprep20_2mm_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin2009cAsym','coarse',2);
end
varname = 'atlas_obj';
docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin2009cAsym','coarse',2);

case {'canlab2023_coarse_fsl6_2mm', 'canlab2023_coarse_fsl6', 'canlab2023_fsl6_2mm', 'canlab2023_fsl6'}
savefile='CANLab2023_coarse_fsl6_2mm_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin6Asym','coarse',2);
end
varname = 'atlas_obj';
docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin6Asym','coarse',2);

case {'canlab2023_coarse_fmriprep20_1mm', 'canlab2023_coarse_1mm', 'canlab2023_fmriprep20_1mm', 'canlab2023_1mm'}
savefile='CANLab2023_coarse_fmriprep20_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin2009cAsym','coarse',1);
end
varname = 'atlas_obj';
docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin2009cAsym','coarse',1);

case {'canlab2023_coarse_fsl6_1mm', 'canlab2023_fsl6_1mm'}
savefile='CANLab2023_coarse_fsl6_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin6Asym','coarse',1);
end
varname = 'atlas_obj';
docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin6Asym','coarse',1);

case {'canlab2023_fine_fmriprep20_2mm', 'canlab2023_fine_fmriprep20','canlab2023_fine_2mm', 'canlab2023_fine'}
savefile='CANLab2023_fine_fmriprep20_2mm_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin2009cAsym','fine',2);
end
varname = 'atlas_obj';
docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin2009cAsym','fine',2);

case {'canlab2023_fine_fsl6_2mm', 'canlab2023_fine_fsl6'}
savefile='CANLab2023_fine_fsl6_2mm_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin6Asym','fine',2);
end
varname = 'atlas_obj';

docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin6Asym','fine',2);

case {'canlab2023_fine_fmriprep20_1mm', 'canlab2023_fine_1mm'}
savefile='CANLab2023_fine_fmriprep20_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin2009cAsym','fine',1);
end
varname = 'atlas_obj';
docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin2009cAsym','fine',1);

case {'canlab2023_fine_fsl6_1mm'}
savefile='CANLab2023_fine_fsl6_atlas_object.mat';
if isempty(dir(which(savefile))) && ~isempty(dir(which('create_CANLab2023_atlas.m')))
create_CANLab2023_atlas('MNI152NLin6Asym','fine',1);
end
varname = 'atlas_obj';
docreate = true;
create_atlas = @(x1)create_CANLab2023_atlas('MNI152NLin6Asym','fine',1);

otherwise % assume it's a file name
savefile = which(atlas_file_name_or_keyword);
varname = [];

end % switch

atlas_obj = load_atlas_from_file(savefile, varname, verbose);
if ~docreate

atlas_obj = load_atlas_from_file(savefile, varname, verbose);

else
% has creation script, so let's run it if either is true: (1) atlas
% file is missing, (2) atlas is out of date
if isempty(dir(which(savefile)))
% atlas is missing
create_atlas(0);
this_atlas = load_atlas_from_file(savefile, varname, verbose);
else
latest = which(strrep(savefile,'.mat','.latest'));
if exist(latest, 'file') ~= 2
create_atlas(0);
end
fid = fopen(latest);
latest = str2num(char(fread(fid,inf)'));
fclose(fid);

atlas_obj = load_atlas_from_file(savefile, varname, verbose);
if round(latest) ~= round(atlas_obj.additional_info.creation_date)
% evaluation is rounded to the nearest second to deal with
% floating point issues. If there's an atlas 1s newer availble
% then it means we rebuild the atlas to get it.
if verbose
fprintf('Updating atlas...\n');
end
create_atlas(0);

atlas_obj = load_atlas_from_file(savefile, varname, verbose);
end
end
end


end % function

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