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Merge pull request #60 from Remi-Gau/remi-dev
fix RFX issues and add credits
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‎README.md‎

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[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline)
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[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors)
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[![DOI](https://zenodo.org/badge/208231636.svg)](https://zenodo.org/badge/latestdoi/208231636)
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# Instructions for SPM12 Preprocessing Pipeline
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‎batch.m‎

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% __ ____ ____ _ _ _
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% / _)( _ \( _ \ | | / \ | )
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% ( (_ )___/ )___/ | |_ / _ \ | \
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% \__)(__) (__) |___||_/ \_||__)
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%
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% Thank you for using the CPP lap pipeline - version 0.0.3.
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%
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% Current list of contributors includes
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% Mohamed Rezk
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% Rémi Gau
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% Olivier Collignon
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% Ane Gurtubay
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% Marco Barilari
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%
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% Please cite using the following DOI:
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% https://doi.org/10.5281/zenodo.3554332
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%
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% For bug report, suggestions for improvements or contributions see our github repo:
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% https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline
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clear
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clc
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@@ -18,16 +38,16 @@
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checkDependencies();
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% copy raw folder into derivatives folder
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BIDS_copyRawFolder(opt, 1)
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% BIDS_copyRawFolder(opt, 1)
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% preprocessing
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BIDS_STC(opt);
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BIDS_SpatialPrepro(opt);
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BIDS_Smoothing(6, opt);
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% BIDS_STC(opt);
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% BIDS_SpatialPrepro(opt);
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% BIDS_Smoothing(6, opt);
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% subject level Univariate
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BIDS_FFX(1, 6, opt);
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BIDS_FFX(2, 6, opt);
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% BIDS_FFX(1, 6, opt);
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% BIDS_FFX(2, 6, opt);
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% group level univariate
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BIDS_RFX(1, 6, 6)
@@ -36,9 +56,9 @@
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BIDS_Results(6, 6, opt, 0)
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% subject level multivariate
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isMVPA=1;
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BIDS_FFX(1, 6, opt, isMVPA);
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BIDS_FFX(2, 6, opt, isMVPA);
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make4Dmaps(6,opt)
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% isMVPA=1;
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% BIDS_FFX(1, 6, opt, isMVPA);
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% BIDS_FFX(2, 6, opt, isMVPA);
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% make4Dmaps(6,opt)
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‎getOption.m‎

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@@ -1,4 +1,25 @@
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function opt = getOption()
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% __ ____ ____ _ _ _
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% / _)( _ \( _ \ | | / \ | )
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% ( (_ )___/ )___/ | |_ / _ \ | \
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% \__)(__) (__) |___||_/ \_||__)
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%
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% Thank you for using the CPP lap pipeline - version 0.0.3.
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%
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% Current list of contributors includes
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% Mohamed Rezk
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% Rémi Gau
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% Olivier Collignon
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% Ane Gurtubay
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% Marco Barilari
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%
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% Please cite using the following DOI:
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% https://doi.org/10.5281/zenodo.3554332
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%
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% For bug report, suggestions for improvements or contributions see our github repo:
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% https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline
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% returns a structure that contains the options chosen by the user to run
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% slice timing correction, pre-processing, FFX, RFX.
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@@ -9,18 +30,34 @@
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% group of subjects to analyze
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opt.groups = {''};
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% suject to run in each group
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opt.subjects = {[1:2]};
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opt.subjects = {[]};
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% task to analyze
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opt.taskName = 'MotionDecoding';
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opt.taskName = 'visMotion';
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% The directory where the data are located
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opt.dataDir = '/Users/mohamed/Desktop/MotionWorkshop/raw';
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opt.dataDir = '/Users/mohamed/Desktop/Data/raw';
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opt.dataDir = '/home/remi/BIDS/visMotion/derivatives/';
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% specify the model file that contains the contrasts to compute
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opt.model.univariate.file = '/home/remi/github/CPP_BIDS_SPM_pipeline/model-visMotionLoc_smdl.json';
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opt.model.multivariate.file = '';
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% specify the result to compute
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opt.result.Steps(1) = struct(...
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'Level', 'dataset', ...
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'Contrasts', struct(...
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'Name', 'VisMot_gt_VisStat', ... % has to match one of the contrast defined in the model json file
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'Mask', false, ... % this might need improving if a mask is required
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'MC', 'FWE', ... FWE, none, FDR
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'p', 0.05, ...
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'k', 0, ...
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'NIDM', true) );
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% Options for slice time correction
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% If left unspecified the slice timing will be done using the mid-volume acquisition
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% time point as reference.
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opt.JOBS_dir = fullfile(opt.dataDir, '..', 'derivatives', 'SPM12_CPPL', 'JOBS', opt.taskName);
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% specify the model file that contains the contrasts to compute
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opt.model.univariate.file = '/Users/mohamed/Documents/GitHub/BIDS_fMRI_scripts/model-motionDecodingUnivariate_smdl.json';
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opt.model.multivariate.file = '/Users/mohamed/Documents/GitHub/BIDS_fMRI_scripts/model-motionDecodingMultivariate_smdl.json';
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% specify the result to compute
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opt.result.Steps(1) = struct(...
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'Level', 'dataset', ...
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'Contrasts', struct(...
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'Name', 'Vis_U', ... % has to match one of the contrast defined in the model json file
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'Mask', false, ... % this might need improving if a mask is required
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'MC', 'none', ... FWE, none, FDR
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'p', 0.05, ...
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'k', 0, ...
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'NIDM', true) );
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% Save the opt variable as a mat file to load directly in the preprocessing
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% scripts
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save('opt.mat','opt')
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end

‎subfun/BIDS_RFX.m‎

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@@ -80,6 +80,7 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)
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end
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% save the matlabbatch
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[~, ~, ~] = mkdir(JOBS_dir);
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save(fullfile(JOBS_dir, ...
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['jobs_matlabbatch_SPM12_SmoothCon_',...
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num2str(mmConSmoothing),'_',...
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fprintf(1,'Create Mean Struct and Mask IMAGES...')
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% save the matlabbatch
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[~, ~, ~] = mkdir(JOBS_dir);
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save(fullfile(JOBS_dir, ...
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'jobs_matlabbatch_SPM12_CreateMeanStrucMask.mat'), ...
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'matlabbatch')
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% the strrep(Session{j}, 'trial_type.', '') is there to remove
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% 'trial_type.' because contrasts against baseline are renamed
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% at the subject level
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conName = strrep(grpLvlCon{j}, 'trial_type.', '');
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conName = rmTrialTypeStr(grpLvlCon{j});
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con = con+1;
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fprintf(1,'A DIRECTORY WITH THIS NAME ALREADY EXISTED AND WAS OVERWRITTEN, SORRY \n');
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rmdir(fullfile(RFX_FolderName, conName),'s')
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end
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mkdir(fullfile(RFX_FolderName, conName))
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289-
matlabbatch{j}.spm.stats.factorial_design.dir = {...
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fullfile(RFX_FolderName,...
291-
grpLvlCon{j}) };
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matlabbatch{j}.spm.stats.factorial_design.dir = { fullfile(RFX_FolderName, conName) };
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end
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% Go to Jobs directory and save the matlabbatch
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matlabbatch = {};
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for j = 1:size(grpLvlCon,1)
310-
matlabbatch{j}.spm.stats.fmri_est.spmmat = {...
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fullfile(RFX_FolderName,...
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grpLvlCon{j},...
313-
'SPM.mat')};
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conName = rmTrialTypeStr(grpLvlCon{j});
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matlabbatch{j}.spm.stats.fmri_est.spmmat = { fullfile(RFX_FolderName, conName, 'SPM.mat') };
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matlabbatch{j}.spm.stats.fmri_est.method.Classical = 1;
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end
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% ADD/REMOVE CONTRASTS DEPENDING ON YOUR EXPERIMENT AND YOUR GROUPS
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for j = 1:size(grpLvlCon,1)
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matlabbatch{j}.spm.stats.con.spmmat = {...
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fullfile(RFX_FolderName,...
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grpLvlCon{j},...
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'SPM.mat')};
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conName = rmTrialTypeStr(grpLvlCon{j});
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matlabbatch{j}.spm.stats.con.spmmat = {fullfile(RFX_FolderName, conName, 'SPM.mat')};
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matlabbatch{j}.spm.stats.con.consess{1}.tcon.name = 'GROUP';
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matlabbatch{j}.spm.stats.con.consess{1}.tcon.convec = 1;
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matlabbatch{j}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
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end
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356353
end
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function conName = rmTrialTypeStr(conName)
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conName = strrep(conName, 'trial_type.', '');
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end

‎subfun/checkDependencies.m‎

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function checkDependencies()
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% Checks that that the right dependencies are installed. ALso loads the spm defaults.
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printCredits()
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SPM_main = 'SPM12';
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SPM_sub = '7487';

‎subfun/printCredits.m‎

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function printCredits()
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version = '0.0.3';
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contributors = {...
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'Mohamed Rezk',...
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'Rémi Gau', ...
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'Olivier Collignon',...
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'Ane Gurtubay', ...
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'Marco Barilari'};
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DOI_URL = 'https://doi.org/10.5281/zenodo.3554332';
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repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline';
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disp( '____________________________________________________________________________________________');
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disp( '____________________________________________________________________________________________');
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disp( ' ');
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disp( ' __ ____ ____ _ _ _ ');
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disp( ' / _)( _ \( _ \ | | / \ | ) ');
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disp( '( (_ )___/ )___/ | |_ / _ \ | \ ');
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disp( ' \__)(__) (__) |___||_/ \_||__)');
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disp( ' ');
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splash = 'Thank you for using the CPP lap pipeline - version %s. ';
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fprintf(splash, version)
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fprintf('\n\n');
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fprintf('Current list of contributors includes\n')
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for iCont = 1:numel(contributors)
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fprintf(' %s\n', contributors{iCont})
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end
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fprintf('\b\n\n')
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fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)
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fprintf('For bug report, suggestions for improvements or contributions see our github repo: \n %s\n\n', repoURL)
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disp( '____________________________________________________________________________________________');
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disp( '____________________________________________________________________________________________');
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fprintf('\n\n')
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end

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