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ea_checkinstall.m
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ea_checkinstall.m
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function [success, commands] = ea_checkinstall(cmd,checkonly,robot)
success=1;
if ~exist('checkonly','var')
checkonly=0;
end
if ~exist('robot','var')
robot=0;
end
switch cmd
case 'list' % simply return list of installable datasets
success={'Redownload data files'
'Install development version of Lead'
'2009b Nonlinear Flip Transform'
'7T Cardiac Gated FLASH MRI (Backdrop visualization)'
'7T Ex Vivo 100um Brain Atlas (Backdrop visualization)'
'Macroscale Human Connectome Atlas (Yeh 2018)'
'Structural group connectome 20 subjects Gibbs-tracker (Horn 2013)'
'Structural group connectome 169 NKI subjects Gibbs-tracker (Horn 2016)'
'Structural group connectome 32 Adult Diffusion HCP subjects GQI v1.1 (Horn 2017)'
'Structural group connectome 85 PPMI PD-patients GQI v1.1 (Ewert 2017)'
'Functional group connectome 74 PPMI PD-patients, 15 controls (Horn 2017)'};
commands={'leaddata'
'hotfix'
'nlinflip'
'7tcgflash'
'7tev100um'
'macroscalehc'
'groupconnectome2013'
'groupconnectome2016'
'groupconnectome2017'
'groupconnectome_ppmi2017'
'fgroupconnectome_ppmi2017'};
case 'leaddata'
checkf=[ea_space,'bb.nii'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Lead Datafiles',...
[],...
'');
else
disp('Lead datafiles is installed.')
end
case 'nlinflip'
checkf=[ea_space,'fliplr'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('FlipLR',...
[ea_space,'fliplr.zip'],...
'fliplr');
else
disp('2009b asym LR flip transform is installed.')
end
case '7tcgflash'
if exist([ea_space,'backdrops',filesep,'7T_Flash_Horn_2018.mat'], 'file')
movefile([ea_space,'backdrops',filesep,'7T_Flash_Horn_2018.mat'], ...
[ea_space,'backdrops',filesep,'7T_Flash_Horn_2019.mat']);
fid = fopen([ea_space,'backdrops',filesep,'backdrops.txt'], 'r');
text = fread(fid, inf, '*char')';
fclose(fid);
text = strrep(text, '7T_Flash_Horn_2018.mat', '7T_Flash_Horn_2019.mat');
fid = fopen([ea_space,'backdrops',filesep,'backdrops.txt'], 'w');
fwrite(fid, text);
fclose(fid);
end
checkf=[ea_space,'backdrops',filesep,'7T_Flash_Horn_2019.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
ea_mkdir([ea_space,'backdrops']);
success=ea_downloadasset('7T Cardiac Gated Flash MRI',...
[ea_space,'backdrops',filesep,'7T_Flash_Horn_2019.mat'],...
'7tcgflash');
m = matfile([ea_space,'backdrops',filesep,'7T_Flash_Horn_2019.mat'],'Writable',true);
m.fname = [ea_space,'backdrops',filesep,'7T_Flash_Horn_2019.nii'];
fid=fopen([ea_space,'backdrops',filesep,'backdrops.txt'],'a');
fprintf(fid,'%s %s\n','7T_Flash_Horn_2019.mat','7T_Cardiac_Gated_Flash_MRI_(Horn_2019)');
fclose(fid);
else
disp('7T Cardiac Gated FLASH MRI (Backdrop visualization) is installed.')
end
case '7tev100um'
checkf=[ea_space,'backdrops',filesep,'7T_100um_Edlow_2019.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
ea_mkdir([ea_space,'backdrops']);
success=ea_downloadasset('7T Ex Vivo 100um Brain Atlas',...
[ea_space,'backdrops',filesep,'7T_100um_Edlow_2019.mat'],...
'7tev100um');
m = matfile([ea_space,'backdrops',filesep,'7T_100um_Edlow_2019.mat'],'Writable',true);
m.fname = [ea_space,'backdrops',filesep,'7T_100um_Edlow_2019.nii'];
fid=fopen([ea_space,'backdrops',filesep,'backdrops.txt'],'a');
fprintf(fid,'%s %s\n','7T_100um_Edlow_2019.mat','7T_Ex_Vivo_100um_Brain_Atlas_(Edlow_2019)');
fclose(fid);
else
disp('7T Ex Vivo 100um Brain Atlas (Backdrop visualization) is installed.')
end
case 'macroscalehc'
checkf=[ea_space,'atlases',filesep,'Macroscale Human Connectome Atlas (Yeh 2018)',filesep,'atlas_index.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Macroscale Human Connectome Atlas',...
[ea_space,'atlases',filesep,'Macroscale_Human_Connectome_Atlas_Yeh_2018.zip'],...
'macroscalehc');
else
disp('Macroscale Human Connectome Atlas is installed.')
end
case 'bigbrain'
checkf=[ea_space,'bigbrain_2015_100um_bb.nii'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Bigbrain 100um subcortical',...
[ea_space,'bigbrain_2015_100um_bb.nii.gz'],...
'bigbrain');
else
disp('BigBrain is installed.')
end
case 'groupconnectome2013'
checkf=[ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) full',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Structural Group Connectome (Horn 2013)',...
[ea_getconnectomebase('dmri'),'groupconnectome2013.zip'],...
'group2013');
else
disp('Structural Group Connectome (Horn 2013) is installed.')
end
case 'groupconnectome2016'
checkf=[ea_getconnectomebase('dmri'),'Gibbsconnectome_169 (Horn 2016)',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Structural Group Connectome (Horn 2016)',...
[ea_getconnectomebase('dmri'),'groupconnectome2016.zip'],...
'group2016');
else
disp('Structural Group Connectome (Horn 2016) is installed.')
end
case 'groupconnectome2017'
checkf=[ea_getconnectomebase('dmri'),'HCP_MGH_32fold_groupconnectome (Horn 2017)',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Structural Group Connectome (Horn 2017)',...
[ea_getconnectomebase('dmri'),'groupconnectome2017.zip'],...
'group2017');
else
disp('Structural Group Connectome (Horn 2017) is installed.')
end
case 'groupconnectome_ppmi2017'
checkf=[ea_getconnectomebase('dmri'),'PPMI_85 (Ewert 2017)',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Structural Group Connectome (Ewert 2017)',...
[ea_getconnectomebase('dmri'),'groupconnectome_ppmi2017.zip'],...
'group2017_ppmi');
else
disp('Structural Group Connectome (Ewert 2017) is installed.')
end
case 'fgroupconnectome_ppmi2017'
checkf=[ea_getconnectomebase('fmri'),'PPMI 74_15 (Horn 2017)',filesep,'dataset_info.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('Functional Group Connectome (Horn 2017)',...
[ea_getconnectomebase('fmri'),'fgroupconnectome_ppmi2017.zip'],...
'fgroup2017_ppmi');
else
disp('Functional Group Connectome (Horn 2017) is installed.')
end
case 'hotfix'
if ~checkonly
success=ea_hotfix;
end
otherwise
success=0;
end
function success=ea_downloadasset(assetname,destination,id)
if strcmp(assetname,'Lead Datafiles')
ea_update_data('full');
success=1;
else
downloadurl = 'https://www.lead-dbs.org/release/download.php';
success=1;
disp(['Downloading ',assetname,'...'])
if ~exist(fileparts(destination), 'dir')
mkdir(fileparts(destination));
end
try
webopts=weboptions('Timeout',Inf);
websave(destination,downloadurl,'id',id,webopts);
catch
try
urlwrite([downloadurl,'?id=',id],destination,'Timeout',Inf);
catch
success=0;
end
end
[loc,~,ext] = fileparts(destination);
if success
disp(['Installing ',assetname,'...'])
if strcmp(ext,'.gz')
gunzip(destination, loc);
ea_delete(destination);
elseif strcmp(ext,'.zip')
unzip(destination, loc);
ea_delete(destination);
end
else
fprintf(['\nDownload error! You may try to download the file manually from:\n',...
'%s\nand then extract it into %s.\n\n'], [downloadurl,'?id=',id], loc);
msgbox('Please check the command window for more information.','Download error!','Error')
return
end
end
function force=ea_alreadyinstalled(checkf,checkonly,robot)
if ~exist(checkf,'file') % then file not there, should install anyways.
force=1;
return
end
if checkonly % return here.
force=0;
return
end
if ~robot
choice = questdlg('This dataset seems already to be installed. Do you wish to re-download it?', ...
'Redownload Dataset?', ...
'Yes','No','No');
if strcmp(choice,'Yes')
force=1;
else
force=-1;
end
else
force=0;
end