Skip to content

fix RFX issues and add credits #60

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 5 commits into from
Nov 28, 2019
Merged

fix RFX issues and add credits #60

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
dc146bc
Add zenodo DOI badge to readme
Remi-Gau Nov 26, 2019
26b85f9
reorganize getOption to put the lines to modify at the top
Remi-Gau Nov 26, 2019
7c18b13
fix RFX so that it can work on its own
Remi-Gau Nov 26, 2019
9be9fa3
update batch file for RFX only
Remi-Gau Nov 26, 2019
e08c269
Add credits
Remi-Gau Nov 26, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
[![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)
[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat-square)](#contributors)
[![DOI](https://zenodo.org/badge/208231636.svg)](https://zenodo.org/badge/latestdoi/208231636)


# Instructions for SPM12 Preprocessing Pipeline

Expand Down
40 changes: 30 additions & 10 deletions batch.m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,23 @@
% __ ____ ____ _ _ _
% / _)( _ \( _ \ | | / \ | )
% ( (_ )___/ )___/ | |_ / _ \ | \
% \__)(__) (__) |___||_/ \_||__)
%
% 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

clear
clc

Expand All @@ -18,16 +38,16 @@
checkDependencies();

% copy raw folder into derivatives folder
BIDS_copyRawFolder(opt, 1)
% BIDS_copyRawFolder(opt, 1)

% preprocessing
BIDS_STC(opt);
BIDS_SpatialPrepro(opt);
BIDS_Smoothing(6, opt);
% BIDS_STC(opt);
% BIDS_SpatialPrepro(opt);
% BIDS_Smoothing(6, opt);

% subject level Univariate
BIDS_FFX(1, 6, opt);
BIDS_FFX(2, 6, opt);
% BIDS_FFX(1, 6, opt);
% BIDS_FFX(2, 6, opt);

% group level univariate
BIDS_RFX(1, 6, 6)
Expand All @@ -36,9 +56,9 @@
BIDS_Results(6, 6, opt, 0)

% subject level multivariate
isMVPA=1;
BIDS_FFX(1, 6, opt, isMVPA);
BIDS_FFX(2, 6, opt, isMVPA);
make4Dmaps(6,opt)
% isMVPA=1;
% BIDS_FFX(1, 6, opt, isMVPA);
% BIDS_FFX(2, 6, opt, isMVPA);
% make4Dmaps(6,opt)


63 changes: 41 additions & 22 deletions getOption.m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,25 @@
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


% returns a structure that contains the options chosen by the user to run
% slice timing correction, pre-processing, FFX, RFX.

Expand All @@ -9,18 +30,34 @@
% group of subjects to analyze
opt.groups = {''};
% suject to run in each group
opt.subjects = {[1:2]};
opt.subjects = {[]};


% task to analyze
opt.taskName = 'MotionDecoding';
opt.taskName = 'visMotion';


% The directory where the data are located
opt.dataDir = '/Users/mohamed/Desktop/MotionWorkshop/raw';
opt.dataDir = '/Users/mohamed/Desktop/Data/raw';
opt.dataDir = '/home/remi/BIDS/visMotion/derivatives/';


% specify the model file that contains the contrasts to compute
opt.model.univariate.file = '/home/remi/github/CPP_BIDS_SPM_pipeline/model-visMotionLoc_smdl.json';
opt.model.multivariate.file = '';


% specify the result to compute
opt.result.Steps(1) = struct(...
'Level', 'dataset', ...
'Contrasts', struct(...
'Name', 'VisMot_gt_VisStat', ... % has to match one of the contrast defined in the model json file
'Mask', false, ... % this might need improving if a mask is required
'MC', 'FWE', ... FWE, none, FDR
'p', 0.05, ...
'k', 0, ...
'NIDM', true) );


% Options for slice time correction
% If left unspecified the slice timing will be done using the mid-volume acquisition
% time point as reference.
Expand All @@ -40,26 +77,8 @@
opt.JOBS_dir = fullfile(opt.dataDir, '..', 'derivatives', 'SPM12_CPPL', 'JOBS', opt.taskName);


% specify the model file that contains the contrasts to compute
opt.model.univariate.file = '/Users/mohamed/Documents/GitHub/BIDS_fMRI_scripts/model-motionDecodingUnivariate_smdl.json';
opt.model.multivariate.file = '/Users/mohamed/Documents/GitHub/BIDS_fMRI_scripts/model-motionDecodingMultivariate_smdl.json';


% specify the result to compute
opt.result.Steps(1) = struct(...
'Level', 'dataset', ...
'Contrasts', struct(...
'Name', 'Vis_U', ... % has to match one of the contrast defined in the model json file
'Mask', false, ... % this might need improving if a mask is required
'MC', 'none', ... FWE, none, FDR
'p', 0.05, ...
'k', 0, ...
'NIDM', true) );


% Save the opt variable as a mat file to load directly in the preprocessing
% scripts
save('opt.mat','opt')


end
29 changes: 16 additions & 13 deletions subfun/BIDS_RFX.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,7 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)
end

% save the matlabbatch
[~, ~, ~] = mkdir(JOBS_dir);
save(fullfile(JOBS_dir, ...
['jobs_matlabbatch_SPM12_SmoothCon_',...
num2str(mmConSmoothing),'_',...
Expand Down Expand Up @@ -193,6 +194,7 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)
fprintf(1,'Create Mean Struct and Mask IMAGES...')

% save the matlabbatch
[~, ~, ~] = mkdir(JOBS_dir);
save(fullfile(JOBS_dir, ...
'jobs_matlabbatch_SPM12_CreateMeanStrucMask.mat'), ...
'matlabbatch')
Expand Down Expand Up @@ -229,7 +231,7 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)
% the strrep(Session{j}, 'trial_type.', '') is there to remove
% 'trial_type.' because contrasts against baseline are renamed
% at the subject level
conName = strrep(grpLvlCon{j}, 'trial_type.', '');
conName = rmTrialTypeStr(grpLvlCon{j});

con = con+1;

Expand Down Expand Up @@ -284,11 +286,10 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)
fprintf(1,'A DIRECTORY WITH THIS NAME ALREADY EXISTED AND WAS OVERWRITTEN, SORRY \n');
rmdir(fullfile(RFX_FolderName, conName),'s')
end

mkdir(fullfile(RFX_FolderName, conName))

matlabbatch{j}.spm.stats.factorial_design.dir = {...
fullfile(RFX_FolderName,...
grpLvlCon{j}) };
matlabbatch{j}.spm.stats.factorial_design.dir = { fullfile(RFX_FolderName, conName) };

end

% Go to Jobs directory and save the matlabbatch
Expand All @@ -307,10 +308,8 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)
matlabbatch = {};

for j = 1:size(grpLvlCon,1)
matlabbatch{j}.spm.stats.fmri_est.spmmat = {...
fullfile(RFX_FolderName,...
grpLvlCon{j},...
'SPM.mat')};
conName = rmTrialTypeStr(grpLvlCon{j});
matlabbatch{j}.spm.stats.fmri_est.spmmat = { fullfile(RFX_FolderName, conName, 'SPM.mat') };
matlabbatch{j}.spm.stats.fmri_est.method.Classical = 1;
end

Expand All @@ -332,10 +331,8 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)

% ADD/REMOVE CONTRASTS DEPENDING ON YOUR EXPERIMENT AND YOUR GROUPS
for j = 1:size(grpLvlCon,1)
matlabbatch{j}.spm.stats.con.spmmat = {...
fullfile(RFX_FolderName,...
grpLvlCon{j},...
'SPM.mat')};
conName = rmTrialTypeStr(grpLvlCon{j});
matlabbatch{j}.spm.stats.con.spmmat = {fullfile(RFX_FolderName, conName, 'SPM.mat')};
matlabbatch{j}.spm.stats.con.consess{1}.tcon.name = 'GROUP';
matlabbatch{j}.spm.stats.con.consess{1}.tcon.convec = 1;
matlabbatch{j}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
Expand All @@ -354,3 +351,9 @@ function BIDS_RFX(action, mmFunctionalSmoothing, mmConSmoothing, opt, isMVPA)
end

end



function conName = rmTrialTypeStr(conName)
conName = strrep(conName, 'trial_type.', '');
end
1 change: 1 addition & 0 deletions subfun/checkDependencies.m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
function checkDependencies()
% Checks that that the right dependencies are installed. ALso loads the spm defaults.

printCredits()

SPM_main = 'SPM12';
SPM_sub = '7487';
Expand Down
45 changes: 45 additions & 0 deletions subfun/printCredits.m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@
function printCredits()
Copy link
Contributor Author

@Remi-Gau Remi-Gau Nov 26, 2019

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This function will display the credits when the pipeline is run. :-)


version = '0.0.3';

contributors = {...
'Mohamed Rezk',...
'Rémi Gau', ...
'Olivier Collignon',...
'Ane Gurtubay', ...
'Marco Barilari'};

DOI_URL = 'https://doi.org/10.5281/zenodo.3554332';

repoURL = 'https://github.com/cpp-lln-lab/CPP_BIDS_SPM_pipeline';

disp( '____________________________________________________________________________________________');
disp( '____________________________________________________________________________________________');
disp( ' ');
disp( ' __ ____ ____ _ _ _ ');
disp( ' / _)( _ \( _ \ | | / \ | ) ');
disp( '( (_ )___/ )___/ | |_ / _ \ | \ ');
disp( ' \__)(__) (__) |___||_/ \_||__)');
disp( ' ');

splash = 'Thank you for using the CPP lap pipeline - version %s. ';
fprintf(splash, version)
fprintf('\n\n');

fprintf('Current list of contributors includes\n')
for iCont = 1:numel(contributors)
fprintf(' %s\n', contributors{iCont})
end
fprintf('\b\n\n')

fprintf('Please cite using the following DOI: \n %s\n\n', DOI_URL)

fprintf('For bug report, suggestions for improvements or contributions see our github repo: \n %s\n\n', repoURL)


disp( '____________________________________________________________________________________________');
disp( '____________________________________________________________________________________________');

fprintf('\n\n')

end