Amended notebooks and template scripts for the new AFNI permutation a…

…nalyses

figures/lib/download_data_amended.py

@@ -53,25 +53,44 @@ def download_data(nv_collection, study, output_dir):
             )
 
     if study not in ('ds120'):
-        euler_char_files = (
-            euler_char_files +
-            # There is no FSL analysis for ds120
-            ((os.path.join('FSL', 'LEVEL2_amended', 'group.gfeat', 'cope1.feat', 'stats', 'euler_chars.csv'), 'fsl_euler_chars.csv'),) +
-            ((os.path.join('FSL', 'LEVEL2_amended', 'permutation_test', 'euler_chars.csv'), 'fsl_perm_euler_chars.csv'),) +
-            # There is no permutation analysis for ds120
-            ((os.path.join('AFNI', 'LEVEL2', 'permutation_test', 'euler_chars.csv'), 'afni_perm_euler_chars.csv'),) + 
-            ((os.path.join('SPM', 'LEVEL2', 'permutation_test', 'euler_chars.csv'), 'spm_perm_euler_chars.csv'),)
-        )
+        if study not in ('ds001'):
+            euler_char_files = (
+                euler_char_files +
+                # There is no FSL analysis for ds120
+                ((os.path.join('FSL', 'LEVEL2_amended', 'group.gfeat', 'cope1.feat', 'stats', 'euler_chars.csv'), 'fsl_euler_chars.csv'),) +
+                ((os.path.join('FSL', 'LEVEL2_amended', 'permutation_test', 'euler_chars.csv'), 'fsl_perm_euler_chars.csv'),) +
+                ((os.path.join('AFNI', 'LEVEL2', 'permutation_test_AMENDED', 'euler_chars.csv'), 'afni_perm_euler_chars.csv'),) + 
+                ((os.path.join('SPM', 'LEVEL2', 'permutation_test', 'euler_chars.csv'), 'spm_perm_euler_chars.csv'),)
+            )
+
+            cluster_count_files = (
+                cluster_count_files +
+                # There is no FSL analysis for ds120
+                    ((os.path.join('FSL', 'LEVEL2_amended', 'group.gfeat', 'cope1.feat', 'stats', 'cluster_count.csv'), 'fsl_cluster_count.csv'),) +
+                    ((os.path.join('FSL', 'LEVEL2_amended', 'permutation_test', 'cluster_count.csv'), 'fsl_perm_cluster_count.csv'),) +
+                # There is no permutation analysis for ds120
+                ((os.path.join('AFNI', 'LEVEL2', 'permutation_test_AMENDED', 'cluster_count.csv'), 'afni_perm_cluster_count.csv'),) + 
+                ((os.path.join('SPM', 'LEVEL2', 'permutation_test', 'cluster_count.csv'), 'spm_perm_cluster_count.csv'),)
+            )
+        else:
+            euler_char_files = (
+                euler_char_files +
+                # There is no FSL analysis for ds120
+                ((os.path.join('FSL', 'LEVEL2', 'group.gfeat', 'cope1.feat', 'stats', 'euler_chars.csv'), 'fsl_euler_chars.csv'),) +
+                ((os.path.join('FSL', 'LEVEL2', 'permutation_test', 'euler_chars.csv'), 'fsl_perm_euler_chars.csv'),) +
+                ((os.path.join('AFNI', 'LEVEL2', 'permutation_test_AMENDED', 'euler_chars.csv'), 'afni_perm_euler_chars.csv'),) + 
+                ((os.path.join('SPM', 'LEVEL2', 'permutation_test', 'euler_chars.csv'), 'spm_perm_euler_chars.csv'),)
+            )
 
-        cluster_count_files = (
-            cluster_count_files +
-            # There is no FSL analysis for ds120
-            ((os.path.join('FSL', 'LEVEL2_amended', 'group.gfeat', 'cope1.feat', 'stats', 'cluster_count.csv'), 'fsl_cluster_count.csv'),) +
-            ((os.path.join('FSL', 'LEVEL2_amended', 'permutation_test', 'cluster_count.csv'), 'fsl_perm_cluster_count.csv'),) +
-            # There is no permutation analysis for ds120
-            ((os.path.join('AFNI', 'LEVEL2', 'permutation_test', 'cluster_count.csv'), 'afni_perm_cluster_count.csv'),) + 
-            ((os.path.join('SPM', 'LEVEL2', 'permutation_test', 'cluster_count.csv'), 'spm_perm_cluster_count.csv'),)
-        )
+            cluster_count_files = (
+                cluster_count_files +
+                # There is no FSL analysis for ds120
+                    ((os.path.join('FSL', 'LEVEL2', 'group.gfeat', 'cope1.feat', 'stats', 'cluster_count.csv'), 'fsl_cluster_count.csv'),) +
+                    ((os.path.join('FSL', 'LEVEL2', 'permutation_test', 'cluster_count.csv'), 'fsl_perm_cluster_count.csv'),) +
+                # There is no permutation analysis for ds120
+                ((os.path.join('AFNI', 'LEVEL2', 'permutation_test_AMENDED', 'cluster_count.csv'), 'afni_perm_cluster_count.csv'),) + 
+                ((os.path.join('SPM', 'LEVEL2', 'permutation_test', 'cluster_count.csv'), 'spm_perm_cluster_count.csv'),)
+            )
 
 
     for euler_char_file, local_name in euler_char_files:
@@ -152,10 +171,15 @@ def download_data(nv_collection, study, output_dir):
         to_download = (
             afni_images + perm_images + r_squared_images)
     else:
-        # BOLD maps
-        bold_images= (('afni_bold.nii.gz','afni_bold.nii.gz'),
-                      ('fsl_bold_amended.nii.gz','fsl_bold.nii.gz'),
-                      ('spm_bold.nii.gz','spm_bold.nii.gz'))
+        if study not in ('ds001'):
+            # BOLD maps
+            bold_images= (('afni_bold.nii.gz','afni_bold.nii.gz'),
+                          ('fsl_bold_amended.nii.gz','fsl_bold.nii.gz'),
+                          ('spm_bold.nii.gz','spm_bold.nii.gz'))
+        else:
+            bold_images= (('afni_bold.nii.gz','afni_bold.nii.gz'),
+                          ('fsl_bold.nii.gz','fsl_bold.nii.gz'),
+                          ('spm_bold.nii.gz','spm_bold.nii.gz'))
 
         to_download = (
             afni_images + perm_images + bold_images)

scripts/ds001_euler_chars_amended.m

@@ -0,0 +1,28 @@
+base_dir = '/home/maullz/NIDM-Ex/BIDS_Data/RESULTS/SOFTWARE_COMPARISON/';
+study = 'ds001';
+DF = 16-1;
+
+if ~exist('euler_chars', 'file')
+    addpath(fullfile(fileparts(mfilename('fullpath')), 'lib'))
+end 
+
+study_dir = fullfile(base_dir, study);
+spm_stat_file = fullfile(study_dir, 'SPM', 'LEVEL2', 'spmT_0001.nii');
+fsl_stat_file = fullfile(study_dir, 'FSL', 'LEVEL2', 'group.gfeat', 'cope1.feat', 'stats', 'tstat1.nii.gz');
+afni_stat_file = fullfile(study_dir, 'AFNI', 'LEVEL2', '3dMEMA_result_t_stat_masked.nii.gz');
+spm_perm_file = fullfile(study_dir, 'SPM', 'LEVEL2', 'permutation_test', 'snpmT+.img');
+fsl_perm_file = fullfile(study_dir, 'FSL', 'LEVEL2', 'permutation_test', 'OneSampT_tstat1.nii.gz');
+afni_perm_file = fullfile(study_dir, 'AFNI', 'LEVEL2', 'permutation_test_AMENDED', 'perm_ttest++_Clustsim_result_t_stat_masked.nii.gz');
+spm_mask = fullfile(study_dir, 'SPM', 'LEVEL2', 'mask.nii');
+fsl_mask = fullfile(study_dir, 'FSL', 'LEVEL2', 'group.gfeat', 'mask.nii.gz');
+afni_mask = fullfile(study_dir, 'AFNI', 'LEVEL2', 'mask.nii.gz');
+
+euler_array = {spm_stat_file, fsl_stat_file, afni_stat_file, spm_perm_file, fsl_perm_file};
+mask_array  = {spm_mask,      fsl_mask,      afni_mask,      spm_mask,      fsl_mask     };
+
+
+for i=1:length(euler_array)
+	euler_chars(euler_array{i}, mask_array{i});
+end
+
+euler_chars(afni_perm_file,afni_mask,DF);

scripts/ds109_euler_chars_amended.m

@@ -12,7 +12,7 @@
 afni_stat_file = fullfile(study_dir, 'AFNI', 'LEVEL2', '3dMEMA_result_t_stat_masked.nii.gz');
 spm_perm_file = fullfile(study_dir, 'SPM', 'LEVEL2', 'permutation_test', 'snpmT+.img');
 fsl_perm_file = fullfile(study_dir, 'FSL', 'LEVEL2_amended', 'permutation_test', 'OneSampT_tstat1.nii.gz');
-afni_perm_file = fullfile(study_dir, 'AFNI', 'LEVEL2', 'permutation_test', 'perm_ttest++_Clustsim_result_t_stat_masked.nii.gz');
+afni_perm_file = fullfile(study_dir, 'AFNI', 'LEVEL2', 'permutation_test_AMENDED', 'perm_ttest++_Clustsim_result_t_stat_masked.nii.gz');
 spm_mask = fullfile(study_dir, 'SPM', 'LEVEL2', 'mask.nii');
 fsl_mask = fullfile(study_dir, 'FSL', 'LEVEL2_amended', 'group.gfeat', 'mask.nii.gz');
 afni_mask = fullfile(study_dir, 'AFNI', 'LEVEL2', 'mask.nii.gz');

scripts/lib/template_ds001_AFNI_perm_test_AMENDED

@@ -7,35 +7,35 @@ cd $perm_dir
     -frac 1.0
 
 # t-test analysis
-3dttest++ 					       \
-    -Clustsim 1 				       \
-    -prefix perm_ttest++_Clustsim_result.nii.gz        \
-    -prefix_clustsim Clustsim			       \
-    -mask $perm_dir/mask.nii.gz   		       \
-    -setA setA                    		       \
-     	     01 "$level1_dir/sub-01/sub01.results/stats.sub01_REML+tlrc.HEAD[30]" \
-             02 "$level1_dir/sub-02/sub02.results/stats.sub02_REML+tlrc.HEAD[30]" \
-             03 "$level1_dir/sub-03/sub03.results/stats.sub03_REML+tlrc.HEAD[30]" \
-             04 "$level1_dir/sub-04/sub04.results/stats.sub04_REML+tlrc.HEAD[30]" \
-             05 "$level1_dir/sub-05/sub05.results/stats.sub05_REML+tlrc.HEAD[30]" \
-             06 "$level1_dir/sub-06/sub06.results/stats.sub06_REML+tlrc.HEAD[30]" \
-             07 "$level1_dir/sub-07/sub07.results/stats.sub07_REML+tlrc.HEAD[30]" \
-             08 "$level1_dir/sub-08/sub08.results/stats.sub08_REML+tlrc.HEAD[30]" \
-             09 "$level1_dir/sub-09/sub09.results/stats.sub09_REML+tlrc.HEAD[30]" \
-             10 "$level1_dir/sub-10/sub10.results/stats.sub10_REML+tlrc.HEAD[30]" \
-             11 "$level1_dir/sub-11/sub11.results/stats.sub11_REML+tlrc.HEAD[30]" \
-             12 "$level1_dir/sub-12/sub12.results/stats.sub12_REML+tlrc.HEAD[30]" \
-             13 "$level1_dir/sub-13/sub13.results/stats.sub13_REML+tlrc.HEAD[30]" \
-             14 "$level1_dir/sub-14/sub14.results/stats.sub14_REML+tlrc.HEAD[30]" \
-             15 "$level1_dir/sub-15/sub15.results/stats.sub15_REML+tlrc.HEAD[30]" \
-             16 "$level1_dir/sub-16/sub16.results/stats.sub16_REML+tlrc.HEAD[30]" 
+#3dttest++ 					       \
+#    -Clustsim 1 				       \
+#    -prefix perm_ttest++_Clustsim_result.nii.gz        \
+#    -prefix_clustsim Clustsim			       \
+#    -mask $perm_dir/mask.nii.gz   		       \
+#    -setA setA                    		       \
+#     	     01 "$level1_dir/sub-01/sub01.results/stats.sub01_REML+tlrc.HEAD[30]" \
+#             02 "$level1_dir/sub-02/sub02.results/stats.sub02_REML+tlrc.HEAD[30]" \
+#             03 "$level1_dir/sub-03/sub03.results/stats.sub03_REML+tlrc.HEAD[30]" \
+#             04 "$level1_dir/sub-04/sub04.results/stats.sub04_REML+tlrc.HEAD[30]" \
+#             05 "$level1_dir/sub-05/sub05.results/stats.sub05_REML+tlrc.HEAD[30]" \
+#             06 "$level1_dir/sub-06/sub06.results/stats.sub06_REML+tlrc.HEAD[30]" \
+#             07 "$level1_dir/sub-07/sub07.results/stats.sub07_REML+tlrc.HEAD[30]" \
+#             08 "$level1_dir/sub-08/sub08.results/stats.sub08_REML+tlrc.HEAD[30]" \
+#             09 "$level1_dir/sub-09/sub09.results/stats.sub09_REML+tlrc.HEAD[30]" \
+#             10 "$level1_dir/sub-10/sub10.results/stats.sub10_REML+tlrc.HEAD[30]" \
+#             11 "$level1_dir/sub-11/sub11.results/stats.sub11_REML+tlrc.HEAD[30]" \
+#             12 "$level1_dir/sub-12/sub12.results/stats.sub12_REML+tlrc.HEAD[30]" \
+#             13 "$level1_dir/sub-13/sub13.results/stats.sub13_REML+tlrc.HEAD[30]" \
+#             14 "$level1_dir/sub-14/sub14.results/stats.sub14_REML+tlrc.HEAD[30]" \
+#             15 "$level1_dir/sub-15/sub15.results/stats.sub15_REML+tlrc.HEAD[30]" \
+#             16 "$level1_dir/sub-16/sub16.results/stats.sub16_REML+tlrc.HEAD[30]" 
 
 # This can be used to obtain cluster extent threshold from the ClustSim.*.1D table for AFNI versions > 18.2.04
-clust_thrvol=`1d_tool.py -verb 0                                       \
-                        -infile Clustsim.CSimA.NN1_1sided.1D           \
-                        -csim_pthr   0.010                              \
-                        -csim_alpha "0.05"`
-echo "++ The final cluster volume threshold is: $$clust_thrvol"
+#clust_thrvol=`1d_tool.py -verb 0                                       \
+#                        -infile Clustsim.CSimA.NN1_1sided.1D           \
+#                        -csim_pthr   0.010                              \
+#                        -csim_alpha "0.05"`
+#echo "++ The final cluster volume threshold is: $$clust_thrvol"
 
 # Obtaining cluster-forming threshold
 voxstat_thr=`p2dsetstat -quiet                                   \
@@ -57,7 +57,7 @@ echo "++ The voxelwise stat value threshold is: $$voxstat_thr"
     -1Dformat -nosum -1tindex 1 -1dindex 0                             \
     -2thresh -1e+09 $$voxstat_thr  -dxyz=1                             \
     -savemask perm_Positive_clust_mask.nii.gz                          \
-    1.01 752 perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
+    1.01 506 perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
 
 # Binarizing
 3dcalc \
@@ -72,7 +72,7 @@ echo "++ The voxelwise stat value threshold is: $$voxstat_thr"
     -1Dformat -nosum -1tindex 1 -1dindex 0                             \
     -2thresh -$$voxstat_thr 1e+09 -dxyz=1                              \
     -savemask perm_Negative_clust_mask.nii.gz                          \
-    1.01 752 perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
+    1.01 506 perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
 
 # Binarizing
 3dcalc \

scripts/lib/template_ds109_AFNI_perm_test_AMENDED

@@ -62,7 +62,7 @@ echo "++ The voxelwise stat value threshold is: $$voxstat_thr"
     -1Dformat -nosum -1tindex 1 -1dindex 0                             \
     -2thresh -1e+09 $$voxstat_thr  -dxyz=1                             \
     -savemask perm_Positive_clust_mask.nii.gz                          \
-    1.01 892 perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
+    1.01 $$clust_thrvol perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
 
 # Binarizing
 3dcalc \
@@ -77,7 +77,7 @@ echo "++ The voxelwise stat value threshold is: $$voxstat_thr"
     -1Dformat -nosum -1tindex 1 -1dindex 0                             \
     -2thresh -$$voxstat_thr 1e+09 -dxyz=1                              \
     -savemask perm_Negative_clust_mask.nii.gz                          \
-    1.01 892 perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
+    1.01 $$clust_thrvol perm_ttest++_Clustsim_result_t_stat_masked_4d.nii.gz
 
 # Binarizing
 3dcalc \