updates from highres analysis

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "lib/bids-matlab"]
+	path = lib/bids-matlab
+	url = https://github.com/cpp-lln-lab/bids-matlab.git

.travis.yml

@@ -37,6 +37,11 @@ before_install:
   - make -C spm12/src PLATFORM=octave distclean
   - make -C spm12/src PLATFORM=octave
   - make -C spm12/src PLATFORM=octave install
+  # get data
+  - mkdir demo/output
+  - curl http://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.bids.zip --output demo/output/MoAEpilot.zip
+  - unzip demo/output/MoAEpilot.zip -d demo/output/
+
 
 script:
   - octave $OCTFLAGS --eval "runTests"

README.md

@@ -27,6 +27,7 @@
   - [Assumption](#assumption)
   - [Setting up](#setting-up)
     - [getOptions](#getoptions)
+      - [spm_my_defaults](#spm_my_defaults)
     - [model JSON files](#model-json-files)
   - [Order of the analysis](#order-of-the-analysis)
   - [Docker](#docker)
@@ -126,8 +127,20 @@ Set the task to analyze in the BIDS data set
 The directory where your files are located on your computer: make sure you have a copy of the data set as this pipeline will change it.
 `opt.derivativesDir = '/Data/auditoryBIDS/derivatives'`
 
+#### spm_my_defaults
+
+
 Some more SPM options can be set in the `spm_my_defaults.m`.
 
+- Use of FAST and not AR1 for auto-correlation modelisation
+
+Using FAST does not seem to affect results on time series with "normal" TRs but 
+improves results when using sequences: it is therefore used by default in this 
+pipeline.
+
+> Olszowy, W., Aston, J., Rua, C. et al. Accurate autocorrelation modeling 
+> substantially improves fMRI reliability. Nat Commun 10, 1220 (2019). 
+> https://doi.org/10.1038/s41467-019-09230-w
 
 ### model JSON files
 This files allow you to specify which contrasts to run and follow the BIDS statistical model extension and as implement by [fitlins](https://fitlins.readthedocs.io/en/latest/model.html)

batch.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 %   __  ____  ____     _      _    _
 %  / _)(  _ \(  _ \   | |    / \  | )
 % ( (_  )___/ )___/   | |_  / _ \ | \

demo/batch_download_run.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 Remi Gau
+
 % This script will download the dataset from the FIL for the block design SPM
 % tutorial and will run the basic preprocessing, FFX and contrasts on it.
 % Results might be a bit different from those in the manual as some
@@ -67,7 +69,7 @@
 %% Get data
 % fprintf('%-40s:', 'Downloading dataset...');
 % urlwrite(URL, 'MoAEpilot.zip');
-unzip('MoAEpilot.zip', fullfile(WD, 'output'));
+% unzip('MoAEpilot.zip', fullfile(WD, 'output'));
 
 %% Check dependencies
 % If toolboxes are not in the MATLAB Directory and needed to be added to
@@ -84,7 +86,7 @@
 %% Run batches
 isMVPA = 0;
 
-bidsCopyRawFolder(opt, 1);
+% bidsCopyRawFolder(opt, 1);
 bidsSTC(opt);
 bidsSpatialPrepro(opt);
 bidsSmoothing(FWHM, opt);

getOption.m

@@ -1,24 +1,7 @@
-function opt = getOption()
-    %   __  ____  ____     _      _    _
-    %  / _)(  _ \(  _ \   | |    / \  | )
-    % ( (_  )___/ )___/   | |_  / _ \ | \
-    %  \__)(__)  (__)     |___||_/ \_||__)
-    %
-    % Thank you for using the CPP lap pipeline - version 0.0.3.
-    %
-    % Current list of contributors includes
-    %  Mohamed Rezk
-    %  Rémi Gau
-    %  Olivier Collignon
-    %  Ane Gurtubay
-    %  Marco Barilari
-    %
-    % Please cite using the following DOI:
-    %  https://doi.org/10.5281/zenodo.3554332
-    %
-    % For bug report, suggestions for improvements or contributions see our github repo:
-    %  https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
 
+function opt = getOption()
+    % opt = getOption()
     % returns a structure that contains the options chosen by the user to run
     % slice timing correction, pre-processing, FFX, RFX.
 

miss_hit.cfg

@@ -1,11 +1,17 @@
 # styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
 line_length: 100
 regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*" # almost anything goes in the root folder
-suppress_rule: "copyright_notice"
 exclude_dir: "lib"
+copyright_entity: "JH"
+copyright_entity: "DSS"
+copyright_entity: "Agah Karakuzu"
+copyright_entity: "Olivier Collignon"
+copyright_entity: "Mohamed Rezk"
+copyright_entity: "Remi Gau"
+copyright_entity: "CPP BIDS SPM-pipeline developpers"
 
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
-metric "file_length": limit 300
-metric "cyc": limit 15
-metric "parameters": limit 4
+metric "file_length": limit 400
+metric "cyc": limit 12
+metric "parameters": limit 6

runTests.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 warning('OFF');
 
 addpath(fullfile(pwd, 'spm12'));

spm_my_defaults.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function spm_my_defaults
     % This is where we set the defautls we want to use.
     % These will overide the spm defaults.

src/concatBetaImgTmaps.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function concatBetaImgTmaps(funcFWHM, opt, deleteIndBeta, deleteIndTmaps)
     % concatBetaImgTmaps(funcFWHM, opt, deleteIndBeta, deleteIndTmaps)
     %

src/convertOnsetTsvToMat.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function fullpathOnsetFileName = convertOnsetTsvToMat(opt, tsvFile, isMVPA)
     %% Converts a tsv file to an onset file suitable for SPM ffx analysis
     % The scripts extracts the conditions' names, onsets, and durations, and
@@ -12,6 +14,7 @@
             'This onset tsv file deos not exist:', ...
             tsvFile);
         error(errorStruct);
+
     end
 
     % Read the tsv file

src/createAndReturnOnsetFile.m

@@ -1,19 +1,27 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function onsetFileName = createAndReturnOnsetFile(opt, subID, funcFWHM, boldFileName, isMVPA)
     % onsetFileName = createAndReturnOnsetFile(opt, boldFileName, prefix, isMVPA)
     %
     % gets the tsv onset file based on the bold file name (removes any prefix)
     %
     % convert the tsv files to a mat file to be used by SPM
 
+    replacePrefixBy = '';
     prefix = getPrefix('FFX', opt, funcFWHM);
     if strcmp(opt.space, 'T1w')
         prefix = getPrefix('FFX_space-T1w', opt, funcFWHM);
     end
 
+    if strcmp(prefix, 'r')
+        prefix = 'rsub-';
+        replacePrefixBy = 'sub-';
+    end
+
     [funcDataDir, boldFileName] = spm_fileparts(boldFileName{1});
 
     tsvFile = strrep(boldFileName, '_bold', '_events.tsv');
-    tsvFile = strrep(tsvFile, prefix, '');
+    tsvFile = strrep(tsvFile, prefix, replacePrefixBy);
     tsvFile = fullfile(funcDataDir, tsvFile);
 
     onsetFileName = convertOnsetTsvToMat(opt, tsvFile, isMVPA);

src/deleteResidualImages.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP BIDS SPM-pipeline developpers
+
 function deleteResidualImages(ffxDir)
     delete(fullfile(ffxDir, 'Res_*.nii'));
 end

src/getBoldFilename.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2020 CPP BIDS SPM-pipeline developpers
+
 function [fileName, subFuncDataDir] = getBoldFilename(varargin)
     % [fileName, subFuncDataDir] = getBoldFilename(BIDS, opt, subID, sessionID, runID)
 

src/getBoldFilenameForFFX.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function [boldFileName, prefix] = getBoldFilenameForFFX(varargin)
     % [boldFileName, prefix] = getFunctionalFiles(BIDS, opt, subID, funcFWHM, iSes, iRun)
     %

src/getData.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function [group, opt, BIDS] = getData(opt, BIDSdir, type)
     % getData checks that all the options specified by the user in getOptions
     % and fills the blank for any that might have been missed out.
@@ -112,7 +114,7 @@
         case 'T1w'
             metadata = spm_BIDS(BIDS, 'metadata', ...
                 'sub', subjects{1}, ...
-                'type', [type]);
+                'type', type);
     end
 
     if iscell(metadata)
@@ -122,44 +124,3 @@
     end
 
 end
-
-function group = getSpecificSubjects(opt, group, iGroup, subjects)
-
-    % if no group or subject was specified we take all of them
-    if numel(opt.groups) == 1 && ...
-            strcmp(group(iGroup).name, '') && ...
-            isempty(opt.subjects{iGroup})
-
-        group(iGroup).subNumber = subjects;
-
-        % if subject ID were directly specified by users we take those
-    elseif strcmp(group(iGroup).name, '') && iscellstr(opt.subjects)
-
-        group(iGroup).subNumber = opt.subjects;
-
-        % if group was specified we figure out which subjects to take
-    elseif ~isempty(opt.subjects{iGroup})
-
-        idx = opt.subjects{iGroup};
-
-        % else we take all subjects of that group
-    elseif isempty(opt.subjects{iGroup})
-
-        % count how many subjects in that group
-        idx = sum(~cellfun(@isempty, strfind(subjects, group(iGroup).name)));
-        idx = 1:idx;
-
-    else
-
-        error('Not sure what to do.');
-
-    end
-
-    % if only indices were specified we get the subject from that group with that
-    if exist('idx', 'var')
-        pattern = [group(iGroup).name '%0' num2str(opt.zeropad) '.0f_'];
-        temp = strsplit(sprintf(pattern, idx), '_');
-        group(iGroup).subNumber = temp(1:end - 1);
-    end
-
-end

src/getFFXdir.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function ffxDir = getFFXdir(subID, funcFWFM, opt, isMVPA)
     % ffxDir = getFFXdir(subID, funcFWFM, opt, isMVPA)
     %

src/getFuncVoxelDims.m

@@ -0,0 +1,25 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
+function [voxDim, opt] = getFuncVoxelDims(opt, subFuncDataDir, prefix, fileName)
+    % [voxDim, opt] = getFuncVoxelDims(opt, subFuncDataDir, prefix, fileName)
+    %
+    %
+
+    % get native resolution to reuse it at normalisation;
+    if ~isempty(opt.funcVoxelDims) % If voxel dimensions is defined in the opt
+        voxDim = opt.funcVoxelDims; % Get the dimension values
+    else
+        % SPM Doesnt deal with nii.gz and all our nii should be unzipped
+        % at this stage
+        hdr = spm_vol(fullfile(subFuncDataDir, [prefix, fileName]));
+        voxDim = diag(hdr(1).mat);
+        % Voxel dimensions are not pure integers before reslicing, therefore
+        % round the dimensions of the functional files to the 1st decimal point
+        voxDim = abs(voxDim(1:3)');
+        voxDim = round(voxDim * 10) / 10;
+        % Add it to opt.funcVoxelDims to have the same value for
+        % all subjects and sessions
+        opt.funcVoxelDims = voxDim;
+    end
+
+end

src/getGrpLevelContrastToCompute.m

@@ -0,0 +1,17 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
+function [grpLvlCon, iStep] = getGrpLevelContrastToCompute(opt, isMVPA)
+
+    model = spm_jsonread(opt.model.univariate.file);
+    if isMVPA
+        model = spm_jsonread(opt.model.multivariate.file);
+    end
+
+    for iStep = 1:length(model.Steps)
+        if strcmp(model.Steps{iStep}.Level, 'dataset')
+            grpLvlCon = model.Steps{iStep}.AutoContrasts;
+            break
+        end
+    end
+
+end

src/getInfo.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function varargout = getInfo(BIDS, subID, opt, info, varargin)
     % for a given BIDS data set, subject identity, and info type,
     % if info = Sessions, this returns name of the sessions and their number

src/getPrefix.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function [prefix, motionRegressorPrefix] = getPrefix(step, opt, funcFWHM)
     % generates prefix to append to file name to look for
 

src/getRFXdir.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function rfxDir = getRFXdir(opt, funcFWHM, conFWHM, contrastName)
     % rfxDir = getRFXdir(opt, funcFWHM, conFWHM, iStep, iCon)
     %

src/getRealignParamFile.m

@@ -1,10 +1,17 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function realignParamFile = getRealignParamFile(opt, fullpathBoldFileName, funcFWHM)
 
     [prefix, motionRegressorPrefix] = getPrefix('FFX', opt, funcFWHM);
     if strcmp(opt.space, 'T1w')
         [prefix, motionRegressorPrefix] = getPrefix('FFX_space-T1w', opt, funcFWHM);
     end
 
+    if strcmp(prefix, 'r')
+        prefix = 'rsub-';
+        motionRegressorPrefix = 'sub-';
+    end
+
     [funcDataDir, boldFileName] = spm_fileparts(fullpathBoldFileName{1});
 
     realignParamFile = strrep(boldFileName, prefix, motionRegressorPrefix);

src/getSliceOrder.m

@@ -1,3 +1,5 @@
+% (C) Copyright 2019 CPP BIDS SPM-pipeline developpers
+
 function sliceOrder = getSliceOrder(opt, verbose)
     % get the slice order information from the BIDS data set or from  getOption
     %