diff --git a/scripts/process_ds001_AFNI.py b/scripts/process_ds001_AFNI.py index d8d03b3..e4fafa9 100644 --- a/scripts/process_ds001_AFNI.py +++ b/scripts/process_ds001_AFNI.py @@ -8,6 +8,7 @@ from lib.afni_processing import run_permutation_test from lib.afni_processing import mean_mni_images from lib.afni_processing import run_SSWarper +from lib.afni_processing import run_orthogonalize raw_dir = '/home/maullz/NIDM-Ex/BIDS_Data/DATA/BIDS/ds001_R2.0.4' @@ -66,10 +67,14 @@ cond_files = create_afni_onset_files(raw_dir, onset_dir, conditions, removed_TR_time) SSWarper_template = os.path.join(cwd, 'lib', 'template_AFNI_SSWarper') +orthogonalize_template = os.path.join(cwd, 'lib', 'template_AFNI_orthogonalize') sub_level_template = os.path.join(cwd, 'lib', 'template_ds001_AFNI_level1') grp_level_template = os.path.join(cwd, 'lib', 'template_ds001_AFNI_level2') perm_template = os.path.join(cwd, 'lib', 'template_ds001_AFNI_perm_test') +# Orthogonalize conditions following the original study +run_orthogonalize(preproc_dir, onset_dir, orthogonalize_template) + # Run SSWarper AFNI command on each subject to strip skull and warp to MNI template run_SSWarper(preproc_dir, SSWarper_template) diff --git a/scripts/process_ds001_AFNI.sh b/scripts/process_ds001_AFNI.sh index 0b03fee..9e99f98 100644 --- a/scripts/process_ds001_AFNI.sh +++ b/scripts/process_ds001_AFNI.sh @@ -2,12 +2,12 @@ #$ -V #$ -S /bin/bash #$ -l h_vmem=16G -#$ -l h_rt=05:30:00 +#$ -l h_rt=19:30:00 #$ -o /home/maullz/NIDM-Ex/BIDS_Data/RESULTS/SOFTWARE_COMPARISON/log #$ -e /home/maullz/NIDM-Ex/BIDS_Data/RESULTS/SOFTWARE_COMPARISON/log . /etc/profile -module add afni +module add afni/18.1.09 python /home/maullz/NIDM-Ex/BIDS_Data/RESULTS/SOFTWARE_COMPARISON/scripts/process_ds001_AFNI.py diff --git a/scripts/process_ds001_FSL.py b/scripts/process_ds001_FSL.py index 35266e0..6e4e856 100644 --- a/scripts/process_ds001_FSL.py +++ b/scripts/process_ds001_FSL.py @@ -32,7 +32,7 @@ # Copy raw anatomical and functional data to the preprocessing directory and # run BET on the anatomical images -#copy_and_BET(raw_dir, preproc_dir) +copy_and_BET(raw_dir, preproc_dir) # Directory to store the onset files onsetDir = os.path.join(fsl_dir, 'ONSETS') @@ -49,7 +49,7 @@ ('control_pumps_RT', ('control_pumps_demean', 'response_time'))) # Create 3-columns onset files based on BIDS tsv files -#cond_files = create_fsl_onset_files(raw_dir, onsetDir, conditions, removed_TR_time) +cond_files = create_fsl_onset_files(raw_dir, onsetDir, conditions, removed_TR_time) run_level_fsf = os.path.join(cwd, 'lib', 'template_ds001_FSL_level1.fsf') sub_level_fsf = os.path.join(cwd, 'lib', 'template_ds001_FSL_level2.fsf') @@ -57,13 +57,13 @@ perm_template = os.path.join(cwd, 'lib', 'template_ds001_FSL_perm_test') # Run a GLM for each fMRI run of each subject -#run_run_level_analyses(preproc_dir, run_level_fsf, level1_dir, cond_files) +run_run_level_analyses(preproc_dir, run_level_fsf, level1_dir, cond_files) # Run a GLM combining all the fMRI runs of each subject -#run_subject_level_analyses(level1_dir, sub_level_fsf, level2_dir) +run_subject_level_analyses(level1_dir, sub_level_fsf, level2_dir) # Run the group-level GLM -#run_group_level_analysis(level2_dir, grp_level_fsf, level3_dir, '1') +run_group_level_analysis(level2_dir, grp_level_fsf, level3_dir, '1') # Run a permutation test run_permutation_test(level1_dir, perm_dir, perm_template) diff --git a/scripts/process_ds001_SPM.m b/scripts/process_ds001_SPM.m index 49961a9..eb38434 100644 --- a/scripts/process_ds001_SPM.m +++ b/scripts/process_ds001_SPM.m @@ -48,5 +48,5 @@ spm('defaults','FMRI'); run_subject_level_analyses(study_dir, preproc_dir, 'template_ds001_SPM_level1', level1_dir, num_ignored_volumes, TR); run_group_level_analysis(level1_dir, 'template_ds001_SPM_level2', level2_dir, '0001'); -%run_permutation_test(level1_dir, 'template_ds001_SPM_perm_test', perm_dir, '0001'); -%mean_mni_images(preproc_dir, level1_dir, mni_dir); \ No newline at end of file +run_permutation_test(level1_dir, 'template_ds001_SPM_perm_test', perm_dir, '0001'); +mean_mni_images(preproc_dir, level1_dir, mni_dir); diff --git a/scripts/process_ds109_FSL.py b/scripts/process_ds109_FSL.py index a34ca5e..bd2a0b3 100644 --- a/scripts/process_ds109_FSL.py +++ b/scripts/process_ds109_FSL.py @@ -36,7 +36,7 @@ # Copy raw anatomical and functional data to the preprocessing directory and # run BET on the anatomical images -#copy_and_BET(raw_dir, preproc_dir, subject_ids) +copy_and_BET(raw_dir, preproc_dir, subject_ids) # Directory to store the onset files onsetDir = os.path.join(fsl_dir, 'ONSETS') @@ -49,7 +49,7 @@ ('false_photo_question', ('false photo question', 'duration'))) # Create 3-columns onset files based on BIDS tsv files -#cond_files = create_fsl_onset_files(raw_dir, onsetDir, conditions, removed_TR_time, subject_ids) +cond_files = create_fsl_onset_files(raw_dir, onsetDir, conditions, removed_TR_time, subject_ids) run_level_fsf = os.path.join(cwd, 'lib', 'template_ds109_FSL_level1.fsf') sub_level_fsf = os.path.join(cwd, 'lib', 'template_ds109_FSL_level2.fsf') @@ -57,16 +57,16 @@ perm_template = os.path.join(cwd, 'lib', 'template_ds109_FSL_perm_test') # Run a GLM for each fMRI run of each subject -#run_run_level_analyses(preproc_dir, run_level_fsf, level1_dir, cond_files) +run_run_level_analyses(preproc_dir, run_level_fsf, level1_dir, cond_files) # Run a GLM combining all the fMRI runs of each subject -#run_subject_level_analyses(level1_dir, sub_level_fsf, level2_dir) +run_subject_level_analyses(level1_dir, sub_level_fsf, level2_dir) # Run the group-level GLM -#run_group_level_analysis(level2_dir, grp_level_fsf, level3_dir, '1') +run_group_level_analysis(level2_dir, grp_level_fsf, level3_dir, '1') # Run a permutation test run_permutation_test(level1_dir, perm_dir, perm_template) # Create mean and standard deviations maps of the mean func and anat images in MNI space -#mean_mni_images(preproc_dir, level1_dir, mni_dir) +mean_mni_images(preproc_dir, level1_dir, mni_dir) diff --git a/scripts/process_ds109_SPM.m b/scripts/process_ds109_SPM.m index f6bc99a..c120282 100644 --- a/scripts/process_ds109_SPM.m +++ b/scripts/process_ds109_SPM.m @@ -46,5 +46,5 @@ spm('defaults','FMRI'); run_subject_level_analyses(study_dir, preproc_dir, 'template_ds109_SPM_level1', level1_dir, num_ignored_volumes, TR, subject_ids); run_group_level_analysis(level1_dir, 'template_ds109_SPM_level2', level2_dir, '0001'); -%run_permutation_test(level1_dir, 'template_ds109_SPM_perm_test', perm_dir, '0001'); -%mean_mni_images(preproc_dir, level1_dir, mni_dir); \ No newline at end of file +run_permutation_test(level1_dir, 'template_ds109_SPM_perm_test', perm_dir, '0001'); +mean_mni_images(preproc_dir, level1_dir, mni_dir); diff --git a/scripts/process_ds120_AFNI.py b/scripts/process_ds120_AFNI.py index a7e9020..44acba2 100644 --- a/scripts/process_ds120_AFNI.py +++ b/scripts/process_ds120_AFNI.py @@ -49,7 +49,7 @@ # Copy raw anatomical and functional data to the preprocessing directory and # run BET on the anatomical images -#copy_raw(raw_dir, preproc_dir, subject_ids) +copy_raw(raw_dir, preproc_dir, subject_ids) # Directory to store the onset files onset_dir = os.path.join(afni_dir, 'ONSETS') @@ -63,20 +63,20 @@ ('reward', ('reward_resp', 'duration'))) # Create onset files based on BIDS tsv files -#cond_files = create_afni_onset_files(raw_dir, onset_dir, conditions, removed_TR_time, subject_ids) +cond_files = create_afni_onset_files(raw_dir, onset_dir, conditions, removed_TR_time, subject_ids) SSWarper_template = os.path.join(cwd, 'lib', 'template_AFNI_SSWarper') sub_level_template = os.path.join(cwd, 'lib', 'template_ds120_AFNI_level1') grp_level_template = os.path.join(cwd, 'lib', 'template_ds120_AFNI_level2') # Run SSWarper AFNI command on each subject to strip skull and warp to MNI template -#run_SSWarper(preproc_dir, SSWarper_template) +run_SSWarper(preproc_dir, SSWarper_template) # Run a GLM combining all the fMRI runs of each subject -#run_subject_level_analyses(preproc_dir, onset_dir, level1_dir, sub_level_template) +run_subject_level_analyses(preproc_dir, onset_dir, level1_dir, sub_level_template) # Run the group-level GLM run_group_level_analysis(level1_dir, level2_dir, grp_level_template) # Create mean and standard deviations maps of the mean func and anat images in MNI space -#mean_mni_images(preproc_dir, level1_dir, mni_dir) +mean_mni_images(preproc_dir, level1_dir, mni_dir) diff --git a/scripts/process_ds120_FSL.py b/scripts/process_ds120_FSL.py index cdd1f66..311cf47 100644 --- a/scripts/process_ds120_FSL.py +++ b/scripts/process_ds120_FSL.py @@ -33,7 +33,7 @@ # Copy raw anatomical and functional data to the preprocessing directory and # run BET on the anatomical images -#copy_and_BET(raw_dir, preproc_dir, subject_ids) +copy_and_BET(raw_dir, preproc_dir, subject_ids) # Directory to store the onset files onsetDir = os.path.join(fsl_dir, 'ONSETS') @@ -44,18 +44,18 @@ ('reward', ('reward_resp', 'duration'))) # Create 3-columns onset files based on BIDS tsv files -#cond_files = create_fsl_onset_files(raw_dir, onsetDir, conditions, removed_TR_time, subject_ids) +cond_files = create_fsl_onset_files(raw_dir, onsetDir, conditions, removed_TR_time, subject_ids) run_level_fsf = os.path.join(cwd, 'lib', 'template_ds120_FSL_level1.fsf') -# sub_level_fsf = os.path.join(cwd, 'lib', 'template_ds120_FSL_level2.fsf') -# grp_level_fsf = os.path.join(cwd, 'lib', 'template_ds120_FSL_level3.fsf') +sub_level_fsf = os.path.join(cwd, 'lib', 'template_ds120_FSL_level2.fsf') +grp_level_fsf = os.path.join(cwd, 'lib', 'template_ds120_FSL_level3.fsf') # Run a GLM for each fMRI run of each subject -#run_run_level_analyses(preproc_dir, run_level_fsf, level1_dir, cond_files) +run_run_level_analyses(preproc_dir, run_level_fsf, level1_dir, cond_files) # Run a GLM combining all the fMRI runs of each subject -#run_subject_level_analyses(level1_dir, sub_level_fsf, level2_dir) +run_subject_level_analyses(level1_dir, sub_level_fsf, level2_dir) # Run the group-level GLM -#run_group_level_analysis(level2_dir, grp_level_fsf, level3_dir, '1') +run_group_level_analysis(level2_dir, grp_level_fsf, level3_dir, '1') diff --git a/scripts/process_ds120_SPM.m b/scripts/process_ds120_SPM.m index b3b9da0..3949a39 100644 --- a/scripts/process_ds120_SPM.m +++ b/scripts/process_ds120_SPM.m @@ -50,4 +50,4 @@ spm('defaults','FMRI'); run_subject_level_analyses(study_dir, preproc_dir, 'template_ds120_SPM_level1', level1_dir, num_ignored_volumes, TR, subject_ids); run_group_level_analysis(level1_dir, 'template_ds120_SPM_level2', level2_dir, '0001'); -%mean_mni_images(preproc_dir, level1_dir, mni_dir); \ No newline at end of file +mean_mni_images(preproc_dir, level1_dir, mni_dir);