GitHub - martaxavier/fMRI-Preprocessing

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Name		Name	Last commit message	Last commit date
Latest commit History 32 Commits
MATLAB_SCRIPTS		MATLAB_SCRIPTS
STANDARD		STANDARD
.gitignore		.gitignore
README.txt		README.txt
clean_fix_noise.sh		clean_fix_noise.sh
clean_ica_reg_noise.sh		clean_ica_reg_noise.sh
compute_dice.sh		compute_dice.sh
extract_rsns_features.sh		extract_rsns_features.sh
extract_rsns_group_features.sh		extract_rsns_group_features.sh
list_smith_rsns.txt		list_smith_rsns.txt
list_yeo_rsns.txt		list_yeo_rsns.txt
main1.sh		main1.sh
main2.sh		main2.sh
motionpars_expansions.sh		motionpars_expansions.sh
motionpars_expansions_fsl.sh		motionpars_expansions_fsl.sh
perform_bet_fast.sh		perform_bet_fast.sh
perform_fix.sh		perform_fix.sh
perform_group_ica.sh		perform_group_ica.sh
perform_group_ica2.sh		perform_group_ica2.sh
perform_ica.sh		perform_ica.sh
perform_nuisance_reg.sh		perform_nuisance_reg.sh
perform_singlesession_ica.sh		perform_singlesession_ica.sh
perform_spatial_smoothing.sh		perform_spatial_smoothing.sh
perform_temporal_hpf.sh		perform_temporal_hpf.sh
perform_temporal_hpf_motionpars.sh		perform_temporal_hpf_motionpars.sh
preprocess.sh		preprocess.sh
preprocess_mig.sh		preprocess_mig.sh
scripty.sh		scripty.sh
scripty_reg.sh		scripty_reg.sh
settings_dataset.sh		settings_dataset.sh
settings_pipeline.sh		settings_pipeline.sh
transptxt.sh		transptxt.sh

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# fMRI-Preprocessing

STEP 1: check settings_dataset.sh to check if dataset specs are ok
STEP 2: open main1.sh and define input dataset, task and run 
STEP 3: run main1.sh
STEP 4: classify unknown components returned by fix and edit .txt in output directory mel.ica
STEP 5: open main2.sh and define input dataset, task, run, cleanup pipeline and registration flag 
STEP 6: run main2.sh
STEP 7: run perform_group_ica.sh (preferable) or perform_singlesession_ica.sh to perform a group ica or subject ica analysis (open first to edit input variables)
STEP 8 (GROUP ICA): open perform_group_ica2.sh and define input reference RSN template + run perform_group_ica2.sh (edit other input variables as well) 
STEP 8 (SUBJECT ICA): open compute_dice.sh and define input reference RSN template + run compute_dice.sh
STEP 9: (GROUP ICA): run extract_rsns_group_features.sh (open first to edit input variables) 
STEP 9: (SUBJECT ICA): run extract_rsns_features.sh (open first to edit input variables)