Experiment Configuration and Data Analysis for fMRI Preprocessing and Analysis
Configure and create files containing experiment information, link subjects to functional/anatomical files, define session designs, preprocessing steps, model information, contrasts of interest, and run scripts for importing, preprocessing, and analyzing fMRI data.
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FrankLab fMRI preprocessing/QA/first-level analysis scripts
Summary Create configuration files containing all relevant info about your experiment SubjectInfoData.cfg (one per subject) point to functional/anatomical files; session design files SessionInfo.cfg (one per different session/run) condition names, onsets/durations PreprocInfo.cfg Preprocessing steps & details ModelInfo.cfg Model name, contrasts of interest Run FL scripts to import/preprocess/analyze your data fl PREPROC fl MODEL fl QACREATE fl QAPLOT
Summary Create configuration files containing all relevant info about your experiment SubjectInfoData.cfg (one per subject) point to functional/anatomical files; session design files SessionInfo.cfg (one per different session/run) condition names, onsets/durations PreprocInfo.cfg Preprocessing steps & details ModelInfo.cfg Model name, contrasts of interest Run FL scripts to import/preprocess/analyze your data fl PREPROC fl MODEL fl QACREATE fl QAPLOT
fl('PREPROC',...) runs preprocessing steps Configuration (.cfg) file format e.g. %% EXAMPLE .CFG FILE DEFINING SOURCE DATA FILES AND MODEL INFORMATION %% see "help fl_process" for details %% Comments (start by %) #functionals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run00_61.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run01_63.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run02_65.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run03_67.nii #RT 2 #structurals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/mprage/ACE9001_run00_09.nii #design /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_subjectDesign/SubjectDesign_ACE9001.cfg % or (alternative syntax): % #design.runs 1 2 3 4 % #design.files % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignA.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignB.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignC.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignD.cfg
fl('PREPROC',...) runs preprocessing steps Configuration (.cfg) file format e.g. %% EXAMPLE .CFG FILE DEFINING SOURCE DATA FILES AND MODEL INFORMATION %% see "help fl_process" for details %% Field names (start by #) #functionals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run00_61.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run01_63.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run02_65.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run03_67.nii #RT 2 #structurals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/mprage/ACE9001_run00_09.nii #design /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_subjectDesign/SubjectDesign_ACE9001.cfg % or (alternative syntax): % #design.runs 1 2 3 4 % #design.files % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignA.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignB.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignC.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignD.cfg
fl('PREPROC',...) runs preprocessing steps Configuration (.cfg) file format e.g. %% EXAMPLE .CFG FILE DEFINING SOURCE DATA FILES AND MODEL INFORMATION %% see "help fl_process" for details %% #functionals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run00_61.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run01_63.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run02_65.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run03_67.nii #RT 2 Field values (follow fieldname) #structurals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/mprage/ACE9001_run00_09.nii #design /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_subjectDesign/SubjectDesign_ACE9001.cfg % or (alternative syntax): % #design.runs 1 2 3 4 % #design.files % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignA.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignB.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignC.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignD.cfg
fl('PREPROC',...) runs preprocessing steps pipeline_info defines preprocessing pipeline information e.g. % EXAMPLE .CFG FILE DEFINING PREPROCESSING PIPELINE % see "help fl" for details % #steps functional_realign functional_center functional_art functional_segment&normalize_direct functional_smooth functional_smooth structural_center structural_segment&normalize #fwhm 4 6.9282 See example file /project/busplab/software/fl/example_preprocfile.cfg See list of current preprocessing pipelines in /project/busplab/software/fl/misc See help fl for additional details
fl('MODEL',...) runs first-level analysis steps design_info defines first-level model information e.g. %% DEFAULT .CFG FILE DEFINING FIRST-LEVEL MODEL OPTIONS %% see "help fl" for details %% #model_name Speech #contrasts Speech-Baseline Speech 1 Baseline -1 Baseline-Speech Baseline 1 Speech -1 #model_basis hrf+deriv #model_covariates motion art #model_serial AR(1) #hpf 128 #smoothinglevel 1 See example file /project/busplab/software/fl/example_modelfile.cfg See help fl for additional details
fl('MODEL',...) runs first-level analysis steps session_info defines run/session level experiment information e.g. %% EXAMPLE .CFG FILE DEFINING CONDITION TIMING INFORMATION %% see "help fl" for details %% #units secs #onsets 0.00 1 3.00 2 7.00 4 10.00 3 14.00 2 17.00 1 21.00 3 24.00 4 #names Speech_Same Speech_Diff Baseline_Same Baseline_Diff #durations 3 3 3 3 See example file /project/busplab/software/fl/example_sessionfile.cfg Session info can also be imported from a SPM.mat file (and BIDS json file in development) See help fl for additional details
fl('MODEL',...) runs first-level analysis steps subject_info defines subject-specific information (location of functional&anatomical files, TR, ) e.g. %% EXAMPLE .CFG FILE DEFINING SOURCE DATA FILES AND MODEL INFORMATION %% see "help fl_process" for details %% #functionals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run00_61.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run01_63.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run02_65.nii /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/functionals/ACE9001_run03_67.nii #RT 2 #structurals /projectnb/busplab/Experiments/ACE/ACE_reorg/Raw_data/nifti/ACE9001/mprage/ACE9001_run00_09.nii #design /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_subjectDesign/SubjectDesign_ACE9001.cfg % or (alternative syntax): % #design.runs 1 2 3 4 % #design.files % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignA.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignB.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignC.cfg % /projectnb/busplab/Experiments/ACE/ACE_reorg/scripts/ACE_sessionDesign/ACE9001_SessionDesignD.cfg Note: try to keep all information that is subject-specific in a single file Info used by PREPROC saludos Info used by MODEL
Summary Create configuration files containing all relevant info about your experiment SubjectInfoData.cfg (one per subject) point to functional/anatomical files; session design files SessionInfo.cfg (one per different session/run) condition names, onsets/durations PreprocInfo.cfg Preprocessing steps & details ModelInfo.cfg Model name, contrasts of interest Run FL scripts to import/preprocess/analyze your data fl PREPROC fl MODEL fl QACREATE fl QAPLOT
Remember to add FL to your current Matlab path Matlab command: addpath /project/busplab/software/fl Run FL scripts to import/preprocess/analyze your data fl PREPROC fl MODEL fl QACREATE fl QAPLOT
Import / preprocess data fl('PREPROC',...) runs preprocessing steps [,'subject_id'],id : subject IDs = folder names where data will be stored [,'subject_info',files] : subject data information files (one .cfg file per subject; e.g. {'/data/subject1.cfg','/data/subject2.cfg',...}) [,'subject_info',filter] : alternatively, path to subject data information files (e.g. '/data/subject*.cfg') [,'pipeline_info',file] : path to additional preprocessing pipeline information file, if any (e.g. 'example_preprocfile.cfg') [,'overwrite',flag] folders : [1/0] set to true to overwrite existing subject-id folders, or set to false to skip already-existing subject-id [,'parallel',flag] : [1/0] set to true to run using cluster parallelization resources, or set to false to run locally (default: 1) [,'root_folder',folder] default fl data folder) : output folder (where subject-ID folder names will be created/stored; if not specified root_folder will be the Matlab command: fl PREPROC ExperimentCode/SubjectID subject_info SubjectInfoFile.cfg pipeline_info PipelineInfoFile.cfg Subject data will be imported and preprocessed. The details of the raw subject data (e.g. functional/anatomical files) are in SubjectInfoFile.cfg, and the details of the preprocessing pipeline (e.g. preprocessing steps) are in PipelineInfoFile.cfg note: typically SubjectInfoFile.cfg contains subject-specific information (one file per subject), and PipelinInfoFile.cfg contains experiment-specific information (one file per analysis/experiment)
fl('PREPROC',...) runs preprocessing steps Import / preprocess data fl('PREPROC',...) runs preprocessing steps [,'subject_id'],id : subject IDs = folder names where data will be stored [,'subject_info',files] : subject data information files (one .cfg file per subject; e.g. {'/data/subject1.cfg','/data/subject2.cfg',...}) [,'subject_info',filter] : alternatively, path to subject data information files (e.g. '/data/subject*.cfg') [,'pipeline_info',file] : path to additional preprocessing pipeline information file, if any (e.g. 'example_preprocfile.cfg') [,'overwrite',flag] folders : [1/0] set to true to overwrite existing subject-id folders, or set to false to skip already-existing subject-id [,'parallel',flag] : [1/0] set to true to run using cluster parallelization resources, or set to false to run locally (default: 1) [,'root_folder',folder] default fl data folder) : output folder (where subject-ID folder names will be created/stored; if not specified root_folder will be the Example: Matlab command: fl PREPROC example ... subject_info /project/busplab/software/fl/example_datafile_subjectinfo.cfg ... pipeline_info /project/busplab/software/fl/example_preprocfile.cfg subject data will be stored in /projectnb/busplab/FLDATA/example/data/BIDS When preprocessing pipeline is submitted to the cluster (by default) use conn_jobmanager report to check the status of your jobs
fl('PREPROC',...) runs preprocessing steps subject_id defines where the data will be stored e.g. Matlab command: fl PREPROC ACE/C01 subject data will be stored in /projectnb/busplab/FLDATA/Aud/C01 Matlab command: fl PREPROC /mydata/C01 subject data will be stored in /mydata/C01 Matlab command: fl PREPROC C01 root_folder /mydata/ACE subject data will be stored in /mydata/ACE/C01 (by default root_folder points to /project/busplab/software/fl/DATA, a soft link to projectnb/busplab/FLDATA folder)
fl('PREPROC',...) runs preprocessing steps subject_id defines where the data will be stored Additional uses (import/preprocess multiple subjects in a single call): Matlab command: fl PREPROC subject_info /data/DataSubject*.cfg (matching several files /data/DataSubject1.cfg /data/DataSubject2.cfg, ) will import subject_id from filenames (DataSubject1, DataSubject2, ) Matlab command: fl PREPROC /ACE/C%02d subject_info /data/DataSubject*.cfg will import numeric portion of filenames only (ACE/C01, ACE/C02, ) Matlab command: fl( PREPROC ,subject_id, subject_info , subject_info, ) Use functional form of fl calls for more complex entries (e.g. subject_id may be a cell array containing explicit list of all subject_id s that we want to preprocess)
Model estimation fl('MODEL',...) runs first-level analysis steps [,'subject_id'],id : subject IDs = folder names where data is being stored [,'subject_info',files] : subject data information files (one .cfg file per subject; e.g. {'/data/subject1.cfg','/data/subject2.cfg',...}) [,'subject_info',filter] : alternatively, path to subject data information files (e.g. '/data/subject*.cfg') [,'design_info',file] : path to additional first-level design information file, if any (e.g. 'example_modelfile.cfg') [,'overwrite',flag] : [1/0] set to true to overwrite existing subject-id folders, or set to false to skip already-existing subject-id folders Matlab command: fl MODEL ExperimentCode/SubjectID subject_info SubjectInfoFile.cfg design_info DesignInfoFile.cfg Subject data will be analyzed using the experiment design info (e.g. condition onsets/durations) specified in SubjectInfoFile.cfg, and the model estimation options (e.g. contrasts of interest) specified in PipelineInfoFile.cfg note: typically SubjectInfoFile.cfg contains subject-specific information (one file per subject), and DesignInfoFile.cfg contains experiment-specific information (one file per analysis/experiment)
fl('MODEL',...) runs first-level analysis steps Model estimation fl('MODEL',...) runs first-level analysis steps [,'subject_id'],id : subject IDs = folder names where data is being stored [,'subject_info',files] : subject data information files (one .cfg file per subject; e.g. {'/data/subject1.cfg','/data/subject2.cfg',...}) [,'subject_info',filter] : alternatively, path to subject data information files (e.g. '/data/subject*.cfg') [,'design_info',file] : path to additional first-level design information file, if any (e.g. 'example_modelfile.cfg') [,'overwrite',flag] : [1/0] set to true to overwrite existing subject-id folders, or set to false to skip already-existing subject-id folders Example: Matlab command: fl MODEL example subject_info /project/busplab/software/fl/example_datafile_subjectinfo.cfg design_info /project/busplab/software/fl/example_modelfile.cfg subject results will be stored in /projectnb/busplab/FLDATA/example/results/firstlevel/Speech
Quality Assurance fl( QACREATE',...) creates QA plots [,'subject_id'],id : subject IDs = folder names where data is being stored [,'qa_plist',plots] : list of QA plots to create (see "help conn_qaplots" for additional details) Example: Matlab command: fl QACREATE example QA plots will be stored in /projectnb/busplab/FLDATA/example/results/qa Matlab command: fl ALL ExperimentCode/SubjectID subject_info SubjectInfoFile.cfg pipeline_info /project/busplab/software/fl/example_preprocfile.cfg design_info DesignInfoFile.cfg runs PREPROC, MODEL, and QACREATE sequentially
Quality Assurance fl( QAPLOT',...) displays QA plots [,'subject_id'],id : subject IDs = folder names where data is being stored Example: Matlab command: fl QAPLOT example fl QAPLOT ACE note: additional functionality for selective grouping of QA plots in development
Summary Create configuration files containing all relevant info about your experiment SubjectInfoData.cfg (one per subject) point to functional/anatomical files; session design files SessionInfo.cfg (one per different session/run) condition names, onsets/durations PreprocInfo.cfg Preprocessing steps & details ModelInfo.cfg Model name, contrasts of interest Run FL to import/preprocess/analyze your data fl PREPROC fl MODEL fl QACREATE fl QAPLOT
