Skip to content

Commit

Permalink
Merge pull request automaticanalysis#211 from jones-michael-s/BIDS_ex…
Browse files Browse the repository at this point in the history 
…tensions

added acq_details options
  • Loading branch information
@tiborauer
tiborauer authored May 3, 2020
2 parents 05be61d + a6c786c commit 53ef81e
Showing 1 changed file with 118 additions and 55 deletions.
173 changes: 118 additions & 55 deletions aa_engine/aas_processBIDS.m
View file
Original file line number Diff line number Diff line change
@@ -1,13 +1,19 @@
function aap = aas_processBIDS(aap,sessnames,tasknames,SUBJ,regcolumn)
% Allow specify Subjects, Sessions and Events from Brain Imaging Data Structure (BIDS)
%
% aap = aas_processBIDS(aap,[sessnames],[tasknames],[SUBJ],[regcolumn])
%
% Required:
% - aap.directory_conventions.rawdatadir: path to BIDS
%
% Optional:
% - sessnames - cell array with sessions to process (useful if you only want
% some sessions, or if you want to preserve a certain session order)
% - tasknames - cell array of tasks to process - see sessnames
% - SUBJ - cell or char array of subjects to process
% - regcolumn - (default 'trial_type') column in events.tsv to use for first
% level model
%
% Relevant AAP sub-fields:
% - aap.acq_details.input.combinemultiple:
% Combines multiple sessions per subjects (default = false)
Expand All @@ -24,20 +30,23 @@
% - aap.acq_details.numdummies: number of (acquired) dummy scans (default = 0);
% - "repetition_time" (TR) specified in JSON header
%
% Tibor Auer MRC CBU Cambridge 2015
% Update: J Carlin 2018
% the following (optional) fields add flexibility in the handling of
% modeling (i.e., tsv) data. They can be combined as needed:
%
% - aap.acq_details.stripBIDSEventNames: true == strip special characters from event names
% - aap.acq_details.omitNullBIDSEvents: true == do not add "null" events to model
% - aap.acq_details.convertBIDSEventsToUppercase: true == convert event names to uppercase
% - aap.acq_details.maxBIDSEventNameLength: >0 == truncate event names
% - aap.acq_details.omitBIDSmodeling: true == return w/o processing modeling data
%
% CHANGE HISTORY:
%
% aap = aas_processBIDS(aap,[sessnames],[tasknames],[SUBJ],[regcolumn])

function aap = aas_processBIDS(aap,sessnames,tasknames,SUBJ,regcolumn)
% M Jones WashU 2020 -- added acq_details tsv processing options
% J Carlin 2018 -- Update
% Tibor Auer MRC CBU Cambridge 2015 -- new

global BIDSsettings;

oldpath = path;
% we need spm_select here...
addpath(aap.directory_conventions.spmdir);


if ~exist('sessnames','var') || isempty(sessnames)
sessnames = [];
end
Expand All @@ -50,6 +59,7 @@
regcolumn = 'trial_type';
end


BIDSsettings.directories.structDIR = 'anat';
BIDSsettings.directories.functionalDIR = 'func';
BIDSsettings.directories.fieldmapDIR = 'fmap';
Expand Down Expand Up @@ -77,6 +87,8 @@
end
end



%% Process
if BIDSsettings.combinemultiple
aas_log(aap,false,'WARNING: You have selected combining multiple BIDS sessions!');
Expand Down Expand Up @@ -139,11 +151,6 @@
end
end
end

% take SPM off the path again (since the user might end up wanting a different SPM for
% actual data analysis)
path(oldpath);

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% UTILS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand All @@ -156,6 +163,39 @@
fieldmapDIR = BIDSsettings.directories.fieldmapDIR;
diffusionDIR = BIDSsettings.directories.diffusionDIR;

% defaults for acq_details flags

if (isfield(aap.acq_details,'omitBIDSmodeling') && aap.acq_details.omitBIDSmodeling == true)
omitBIDSmodeling = true;
else
omitBIDSmodeling = false;
end

if (isfield(aap.acq_details,'stripBIDSEventNames') && aap.acq_details.stripBIDSEventNames == true)
stripBIDSEventNames = true;
else
stripBIDSEventNames = false;
end

if (isfield(aap.acq_details,'omitNullBIDSEvents') && aap.acq_details.omitNullBIDSEvents == true)
omitNullBIDSEvents = true;
else
omitNullBIDSEvents = false;
end

if (isfield(aap.acq_details,'convertBIDSEventsToUppercase') && aap.acq_details.convertBIDSEventsToUppercase == true)
convertBIDSEventsToUppercase = true;
else
convertBIDSEventsToUppercase = false;
end

if (isfield(aap.acq_details,'maxBIDSEventNameLength') && aap.acq_details.maxBIDSEventNameLength > 0)
maxBIDSEventNameLength = aap.acq_details.maxBIDSEventNameLength;
else
maxBIDSEventNameLength = Inf;
end


% locate first_level modules
stagenumModel(1) = struct('name','aamod_firstlevel_model','ind',...
find(strcmp({aap.tasklist.main.module.name},'aamod_firstlevel_model')));
Expand Down Expand Up @@ -186,7 +226,7 @@
case '.'
case structDIR
if ~toAddData, continue; end
for sfx = {'T1w','T2w'};
for sfx = {'T1w','T2w'}
for image = cellstr(spm_select('FPList',fullfile(sesspath,structDIR),[subjname '.*_' sfx{1} '.*.nii.gz']))'
if isempty(image{1}), continue; end
hdrfname = retrieve_file(fullfile(sesspath,structDIR,[subjname '_' sfx{1},'.json']));
Expand Down Expand Up @@ -244,11 +284,11 @@
ftype = jfname(ind+1:end);
switch ftype
case 'phasediff'
fmap.hdr = {loadjson(f{1})};
if isfield(fmap.hdr{1},'IntendedFor')
fmap.session = cellstr(get_taskname(sesspath,subjname,fmap.hdr.IntendedFor));
fmap.hdr = loadjson(f{1});
if isfield(fmap.hdr,'IntendedFor')
fmap.hdr.session = get_taskname(sesspath,subjname,fmap.hdr.IntendedFor);
else
fmap.session = '*';
fmap.hdr.session = '*';
end
fmap.fname = cellstr(spm_select('FPList',fullfile(sesspath,fieldmapDIR),[strrep(jfname,ftype,'') '.*.nii.gz']));
case 'phase1'
Expand All @@ -265,9 +305,13 @@
tasks = cellfun(@(x)get_taskname(sesspath,subjname,x),allepi,'uniformoutput',0);
outepi = {};
for t = BIDSsettings.tasknames(:)'
thits = cell_index(tasks,t{1});
% thits = cell_index(tasks,t{1});
% cell_index(wawa,'foo') returns true for both 'foo...' and '...foo...'
% (so it can't differentiate between, say, "overt-foo" and "covert-foo")
% use startsWith() instead:
thits = find(startsWith(tasks,t{1}));
if all(thits)==0
aas_log(aap,true,'could not find task %s',t{1});
aas_log(aap,true,sprintf('could not find task %s',t{1}));
end
outepi = [outepi allepi(thits)];
end
Expand Down Expand Up @@ -305,44 +349,63 @@
end

% Model
for thisstage = stagenumModel
if any(thisstage.ind)
iModel = [];
for m = 1:numel(thisstage.ind)
sess = textscan(aap.tasklist.main.module(thisstage.ind(m)).extraparameters.aap.acq_details.selected_sessions,'%s'); sess = sess{1};
if any(strcmp(sess,'*')) || any(strcmp(sess,taskname)), iModel(end+1) = aap.tasklist.main.module(thisstage.ind(m)).index; end
end

if ~TR
aas_log(aap,false,sprintf('WARNING: No (RepetitionTime in) header found for subject %s task/run %s',subjname,taskname))
aas_log(aap,false,'WARNING: No correction of EV onset for dummies is possible!\n')
end

% Search for event file
eventfname = retrieve_file(fullfile(sesspath,functionalDIR,[subjname '_' taskfname '_events.tsv'])); eventfname = eventfname{1}; % ASSUME only one instance
if isempty(eventfname)
aas_log(aap,false,sprintf('WARNING: No event found for subject %s task/run %s\n',subjname,taskname));
else
EVENTS = tsvread(eventfname);
iName = cell_index(EVENTS(1,:),regcolumn);
iOns = cell_index(EVENTS(1,:),'onset');
iDur = cell_index(EVENTS(1,:),'duration');
names = unique(EVENTS(2:end,iName));
onsets = cell(numel(names),1);
durations = cell(numel(names),1);
for t = 2:size(EVENTS,1)
iEV = strcmp(names,EVENTS{t,iName});
onsets{iEV}(end+1) = str2double(EVENTS{t,iOns});
durations{iEV}(end+1) = str2double(EVENTS{t,iDur});

if (omitBIDSmodeling)
aas_log(aap,false,sprintf('INFO: Omitting addevent in aas_processBIDS (change in aap.acq_details.omitBIDSmodeling)'));
else

for thisstage = stagenumModel
if any(thisstage.ind)
iModel = [];
for m = 1:numel(thisstage.ind)
sess = textscan(aap.tasklist.main.module(thisstage.ind(m)).extraparameters.aap.acq_details.selected_sessions,'%s'); sess = sess{1};
if any(strcmp(sess,'*')) || any(strcmp(sess,taskname)), iModel(end+1) = aap.tasklist.main.module(thisstage.ind(m)).index; end
end

if ~TR
aas_log(aap,false,sprintf('WARNING: No (RepetitionTime in) header found for subject %s task/run %s',subjname,taskname))
aas_log(aap,false,'WARNING: No correction of EV onset for dummies is possible!\n')
end
for m = iModel
for e = 1:numel(names)
aap = aas_addevent(aap,sprintf('%s_%05d',thisstage.name,m),subjname,taskname,names{e},onsets{e}-numdummies*TR,durations{e});

% Search for event file
eventfname = retrieve_file(fullfile(sesspath,functionalDIR,[subjname '_' taskfname '_events.tsv'])); eventfname = eventfname{1}; % ASSUME only one instance
if isempty(eventfname)
aas_log(aap,false,sprintf('WARNING: No event found for subject %s task/run %s\n',subjname,taskname));
else
EVENTS = tsvread(eventfname);
iName = cell_index(EVENTS(1,:),regcolumn);
iOns = cell_index(EVENTS(1,:),'onset');
iDur = cell_index(EVENTS(1,:),'duration');
if (stripBIDSEventNames)
EVENTS(2:end,iName) = regexprep(EVENTS(2:end,iName),'[^a-zA-Z0-9]','');
end
names = unique(EVENTS(2:end,iName));
onsets = cell(numel(names),1);
durations = cell(numel(names),1);
for t = 2:size(EVENTS,1)
iEV = strcmp(names,EVENTS{t,iName});
onsets{iEV}(end+1) = str2double(EVENTS{t,iOns});
durations{iEV}(end+1) = str2double(EVENTS{t,iDur});
end
if (convertBIDSEventsToUppercase)
names = upper(names);
end
if (maxBIDSEventNameLength < Inf)
maxlen = maxBIDSEventNameLength;
names = cellfun(@(x) x(1:min(maxlen,length(x))), names,'UniformOutput',false);
end
for m = iModel
for e = 1:numel(names)
if (strcmpi(names{e},'null') && omitNullBIDSEvents)
continue;
end
aap = aas_addevent(aap,sprintf('%s_%05d',thisstage.name,m),subjname,taskname,names{e},onsets{e}-numdummies*TR,durations{e});
end
end
end
end
end
end
end
end
otherwise
aas_log(aap,false,sprintf('NYI: Input %s is not supported',cf{1}));
Expand Down

0 comments on commit 53ef81e

Please sign in to comment.