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tedana clean up and data organization #52

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Mar 6, 2024
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tedana clean up and data organization #52

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52 changes: 24 additions & 28 deletions bids/spmup_BIDS_preprocess.m
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Original file line number Diff line number Diff line change
Expand Up @@ -479,8 +479,8 @@
spm_jsonwrite(new_json,meta,opts);

% add path to tedana output file
new_func{i} = new_tedana_file;
new_func_metadata{i} = subject.func_metadata{idx};
new_func{i,1} = new_tedana_file;
new_func_metadata{i,1} = subject.func_metadata{idx};

spmup_basics(new_tedana_file,'mean') % make a mean image for each task

Expand Down Expand Up @@ -1021,13 +1021,14 @@
% actually do it
if strcmp(options.overwrite_data,'on') || ...
(strcmp(options.overwrite_data,'off') && sum(realign_done)==0)


clear matlabbatch
for frun = size(subject.func,1):-1:1

% index of first echo image belonging current echoset
func_idx = find(arrayfun(@(x) x==frun, [echoinfo(:).echoset], 'UniformOutput', true),1);

clear matlabbatch

matlabbatch{1}.spm.tools.fieldmap.applyvdm.data(frun).scans = subject.func(frun);
if length(which_fmap)==1
matlabbatch{1}.spm.tools.fieldmap.applyvdm.data(frun).vdmfile = options.VDM(which_fmap);
Expand All @@ -1047,8 +1048,8 @@
matlabbatch{1}.spm.tools.fieldmap.applyvdm.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.tools.fieldmap.applyvdm.roptions.mask = 1;
matlabbatch{1}.spm.tools.fieldmap.applyvdm.roptions.prefix = 'u';
spm_jobman('run', matlabbatch); clear matlabbatch
end
spm_jobman('run', matlabbatch); clear matlabbatch
end
end
end
Expand Down Expand Up @@ -1476,23 +1477,24 @@
for frun = 1:size(Normalized_files,1)
[filepath,filename,ext] = fileparts(Normalized_files{frun});
stats_ready{frun,1} = [filepath filesep 's' filename ext];

[filepath,filename,ext] = fileparts(subject.func{frun});
if exist(fullfile(filepath,[filename '.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename '.json']));
elseif exist(fullfile(filepath,[filename(1:end-5) '_space-IXI549_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_space-IXI549_desc-preprocessed_bold.json']));
elseif exist(fullfile(filepath,[filename(1:end-5) '_space-MNI152Lin_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_space-MNI152Lin_desc-preprocessed_bold.json']));
elseif exist(fullfile(filepath,[filename(1:end-5) '_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_desc-preprocessed_bold.json']));
end

if strcmp(options.overwrite_data,'on') || ...
(strcmp(options.overwrite_data,'off') && ~isfield(meta,'smoothingkernel'))

fprintf(' smoothing run %g \n',frun);
V = spm_vol(Normalized_files{frun});
skernel = abs(diag(V(1).mat)); clear V
[filepath,filename,ext] = fileparts(subject.func{frun});
if exist(fullfile(filepath,[filename '.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename '.json']));
elseif exist(fullfile(filepath,[filename(1:end-5) '_space-IXI549_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_space-IXI549_desc-preprocessed_bold.json']));
elseif exist(fullfile(filepath,[filename(1:end-5) '_space-MNI152Lin_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_space-MNI152Lin_desc-preprocessed_bold.json']));
elseif exist(fullfile(filepath,[filename(1:end-5) '_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_desc-preprocessed_bold.json']));
end

if strcmp(options.derivatives,'off') || ...
contains(stats_ready{frun,1},'task-rest','IgnoreCase',true)
Expand Down Expand Up @@ -1640,6 +1642,7 @@
for frun = 1:size(subject.func,1)
if exist(stats_ready{frun},'file')
[filepath,filename,ext] = fileparts(subject.func{frun});

if strcmpi(options.norm,'EPInorm')
newname = fullfile(filepath,[filename(1:end-5) '_space-MNI152Lin_desc-preprocessed_bold' ext]);
else
Expand All @@ -1649,16 +1652,9 @@
subject.func{frun} = newname;

if strcmp(options.QC,'on')
if exist(fullfile(filepath,[filename '.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename '.json']));
elseif exist(fullfile(filepath,[subject.func{frun}(1:end-9) '_space-IXI549_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_space-IXI549_desc-preprocessed_bold.json']));
elseif exist(fullfile(filepath,[subject.func{frun}(1:end-9) '_space-MNI152Lin_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_space-MNI152Lin_desc-preprocessed_bold.json']));
elseif exist(fullfile(filepath,[subject.func{frun}(1:end-9) '_desc-preprocessed_bold.json']),'file')
meta = spm_jsonread(fullfile(filepath,[subject.func{frun}(1:end-9) '_desc-preprocessed_bold.json']));
end


meta = spm_jsonread(fullfile(filepath,[filename(1:end-5) '_desc-preprocessed_bold.json']));

if ~isfield(subject.func_qa{frun},'preproc_outliers')
[~,subject.func_qa{frun}.preproc_outliers] = spmup_volumecorr(newname);
meta.QA.correlation_outliers = subject.func_qa{frun}.preproc_outliers;
Expand Down Expand Up @@ -1782,19 +1778,19 @@
end

% list of prefixes to delete
prefixList = {'st_*', 'rst_*', 'ur*', 'usub*', 'rst_*', 'ur*', 'usub*', 'wusub*', 'ust*', 'wst*', 'wur*', 'wfmag*', 'mean*', 'wmean*'};
prefixList = {'st_*', 'rst_*', 'ur*', 'usub*', 'wusub*', 'ust*', 'wst*', 'wur*', 'wfmag*', 'mean*', 'wmean*'};
for nprefix = 1:numel(prefixList)
tmp = dir(fullfile(filepath,[prefixList{nprefix} ext]));
if ~isempty(tmp)
if exist(tmp(1).name,'file')
if exist(fullfile(tmp(1).folder,tmp(1).name),'file')
toDelete = [toDelete; tmp]; % add to list
end
end
end

tmp = dir(fullfile(filepath,'st_*.mat'));
if ~isempty(tmp)
if exist(tmp(1).name,'file')
if exist(fullfile(tmp(1).folder,tmp(1).name),'file')
toDelete = [toDelete; tmp]; % add to list
end
end
Expand Down
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