Merge branch 'FSL_NL_default' of github.com:AlexBowring/Software_Comp…

…arison into FSL_NL_default

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)
 

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

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')
@@ -49,21 +49,21 @@
     ('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')
 grp_level_fsf = os.path.join(cwd, 'lib', 'template_ds001_FSL_level3.fsf')
 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)

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);
+run_permutation_test(level1_dir, 'template_ds001_SPM_perm_test', perm_dir, '0001');
+mean_mni_images(preproc_dir, level1_dir, mni_dir);

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')
@@ -49,24 +49,24 @@
     ('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')
 grp_level_fsf = os.path.join(cwd, 'lib', 'template_ds109_FSL_level3.fsf')
 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)

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);
+run_permutation_test(level1_dir, 'template_ds109_SPM_perm_test', perm_dir, '0001');
+mean_mni_images(preproc_dir, level1_dir, mni_dir);

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)

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')
 

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);
+mean_mni_images(preproc_dir, level1_dir, mni_dir);