Merge pull request #20 from AlexBowring/amended_FSL_analyses

Amended ds120 analyses
NISOx-BDI · Nov 8, 2020 · 6e33f78 · 6e33f78
2 parents edd62be + 6ee33bc
commit 6e33f78
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Showing 6 changed files with 845 additions and 9 deletions.
diff --git a/figures/ds120_notebook_amended.ipynb b/figures/ds120_notebook_amended.ipynb
diff --git a/figures/lib/download_data_amended.py b/figures/lib/download_data_amended.py
@@ -42,15 +42,26 @@ def download_data(nv_collection, study, output_dir):
             print(url + " already downloaded at " + localzip_rel)
 
     # ---  Copy CSV files with Euler characteristics and Cluster counts
-    euler_char_files = (
-            (os.path.join('AFNI', 'LEVEL2', 'euler_chars.csv'), 'afni_euler_chars.csv'),
-            (os.path.join('SPM', 'LEVEL2', 'euler_chars.csv'), 'spm_euler_chars.csv'),
-            )
-
-    cluster_count_files = (
-            (os.path.join('AFNI', 'LEVEL2', 'cluster_count.csv'), 'afni_cluster_count.csv'),
-            (os.path.join('SPM', 'LEVEL2', 'cluster_count.csv'), 'spm_cluster_count.csv'),
-            )
+    if study not in ('ds120'):
+        euler_char_files = (
+                (os.path.join('AFNI', 'LEVEL2', 'euler_chars.csv'), 'afni_euler_chars.csv'),
+                (os.path.join('SPM', 'LEVEL2', 'euler_chars.csv'), 'spm_euler_chars.csv'),
+                )
+
+        cluster_count_files = (
+                (os.path.join('AFNI', 'LEVEL2', 'cluster_count.csv'), 'afni_cluster_count.csv'),
+                (os.path.join('SPM', 'LEVEL2', 'cluster_count.csv'), 'spm_cluster_count.csv'),
+                )
+    else:
+        euler_char_files = (
+                (os.path.join('AFNI', 'LEVEL2_AMENDED', 'euler_chars.csv'), 'afni_euler_chars.csv'),
+                (os.path.join('SPM', 'LEVEL2', 'euler_chars.csv'), 'spm_euler_chars.csv'),
+                )
+
+        cluster_count_files = (
+                (os.path.join('AFNI', 'LEVEL2_AMENDED', 'cluster_count.csv'), 'afni_cluster_count.csv'),
+                (os.path.join('SPM', 'LEVEL2', 'cluster_count.csv'), 'spm_cluster_count.csv'),
+                ) 
 
     if study not in ('ds120'):
         if study not in ('ds001'):

diff --git a/scripts/ds120_euler_chars_amended.m b/scripts/ds120_euler_chars_amended.m
@@ -0,0 +1,20 @@
+base_dir = '/home/maullz/NIDM-Ex/BIDS_Data/RESULTS/SOFTWARE_COMPARISON/';
+study = 'ds120';
+
+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', 'spmF_0002.nii');
+afni_stat_file = fullfile(study_dir, 'AFNI', 'LEVEL2_AMENDED', 'Group_f_stat_masked.nii.gz');
+spm_mask = fullfile(study_dir, 'SPM', 'LEVEL2', 'mask.nii');
+afni_mask = fullfile(study_dir, 'AFNI', 'LEVEL2_AMENDED', 'mask.nii.gz');
+
+euler_array = {spm_stat_file, afni_stat_file};
+mask_array = {spm_mask, afni_mask};
+
+
+for i=1:length(euler_array)
+	euler_chars_f_statistic(euler_array{i}, mask_array{i});
+end
diff --git a/scripts/ds120_r_squared_maps_amended.m b/scripts/ds120_r_squared_maps_amended.m
@@ -0,0 +1,22 @@
+base_dir = '/home/maullz/NIDM-Ex/BIDS_Data/RESULTS/SOFTWARE_COMPARISON/';
+study = 'ds120';
+% Find degrees of freedom in 2nd-level results
+spm_dof1 = 8;
+spm_dof2 = 142;
+afni_dof1 = 7;
+afni_dof2 = 98;
+
+if ~exist('r_squared_maps', 'file')
+    addpath(fullfile(fileparts(mfilename('fullpath')), 'lib'))
+end 
+
+study_dir = fullfile(base_dir, study);
+spm_stat_file = fullfile(study_dir, 'SPM', 'LEVEL2', 'spmF_0002.nii');
+afni_stat_file = fullfile(study_dir, 'AFNI', 'LEVEL2_AMENDED', 'Group_f_stat_masked.nii.gz');
+spm_mask = fullfile(study_dir, 'SPM', 'LEVEL2', 'mask.nii');
+afni_mask = fullfile(study_dir, 'AFNI', 'LEVEL2_AMENDED', 'mask.nii.gz');
+
+% Creating r_squared_maps, degrees of freedom obtained from second level results
+r_squared_maps(afni_stat_file, afni_mask, afni_dof1, afni_dof2, study_dir);
+r_squared_maps(spm_stat_file, spm_mask, spm_dof1, spm_dof2, study_dir);
+