updated figures/notebooks

NISOx-BDI · Jun 11, 2021 · 93f5da3 · 93f5da3
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diff --git a/figures/All_comparison_figures.pdf b/figures/All_comparison_figures.pdf
diff --git a/figures/ds001_AFNI_FSL/1.png b/figures/ds001_AFNI_FSL/1.png
diff --git a/figures/ds001_AFNI_FSL/7.png b/figures/ds001_AFNI_FSL/7.png
diff --git a/figures/ds001_AFNI_FSL_comparisons.pdf b/figures/ds001_AFNI_FSL_comparisons.pdf
diff --git a/figures/ds001_SPM_FSL/1.png b/figures/ds001_SPM_FSL/1.png
diff --git a/figures/ds001_SPM_FSL/7.png b/figures/ds001_SPM_FSL/7.png
diff --git a/figures/ds001_SPM_FSL_comparisons.pdf b/figures/ds001_SPM_FSL_comparisons.pdf
diff --git a/figures/ds001_notebook.ipynb b/figures/ds001_notebook.ipynb
diff --git a/figures/ds001_permutation_AFNI_FSL/1.png b/figures/ds001_permutation_AFNI_FSL/1.png
diff --git a/figures/ds001_permutation_AFNI_FSL/7.png b/figures/ds001_permutation_AFNI_FSL/7.png
diff --git a/figures/ds001_permutation_AFNI_FSL_comparisons.pdf b/figures/ds001_permutation_AFNI_FSL_comparisons.pdf
diff --git a/figures/ds001_permutation_SPM_FSL/1.png b/figures/ds001_permutation_SPM_FSL/1.png
diff --git a/figures/ds001_permutation_SPM_FSL/7.png b/figures/ds001_permutation_SPM_FSL/7.png
diff --git a/figures/ds001_permutation_SPM_FSL_comparisons.pdf b/figures/ds001_permutation_SPM_FSL_comparisons.pdf
diff --git a/figures/ds109_AFNI_FSL_comparisons.pdf b/figures/ds109_AFNI_FSL_comparisons.pdf
diff --git a/figures/ds109_SPM_FSL_comparisons.pdf b/figures/ds109_SPM_FSL_comparisons.pdf
diff --git a/figures/ds109_notebook.ipynb b/figures/ds109_notebook.ipynb
diff --git a/figures/ds109_permutation_AFNI_FSL_comparisons.pdf b/figures/ds109_permutation_AFNI_FSL_comparisons.pdf
diff --git a/figures/ds109_permutation_SPM_FSL_comparisons.pdf b/figures/ds109_permutation_SPM_FSL_comparisons.pdf
diff --git a/figures/ds120_notebook.ipynb b/figures/ds120_notebook.ipynb
@@ -11,7 +11,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -36,7 +36,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 2,
    "metadata": {
     "scrolled": false
    },
@@ -67,7 +67,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -76,7 +76,7 @@
        "'./input/ds120/spm_afni_subject_level_mask.nii.gz'"
       ]
      },
-     "execution_count": 33,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -192,7 +192,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -214,7 +214,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -249,7 +249,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -335,7 +335,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -367,7 +367,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -402,13 +402,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
+      "pixdim[1,2,3] should be positive; setting to abs of pixdim values\n",
+      "pixdim[1,2,3] should be positive; setting to abs of pixdim values\n",
       "/Users/maullz/Desktop/SC2/figures/lib/bland_altman.py:98: RuntimeWarning: invalid value encountered in greater_equal\n",
       "  white_matter_mask = white_matter >= 0.5\n",
       "/Users/maullz/Desktop/SC2/figures/lib/bland_altman.py:100: RuntimeWarning: invalid value encountered in greater_equal\n",
@@ -447,7 +449,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -471,7 +473,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -495,7 +497,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 42,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -544,7 +546,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.1"
+   "version": "3.6.1"
   }
  },
  "nbformat": 4,

diff --git a/figures/lib/consensus_analysis.py b/figures/lib/consensus_analysis.py
@@ -171,6 +171,7 @@ def consensus_analysis(t_stat_maps, N, study,  max_activation, x_coords, y_coord
     tdata = timg.get_fdata()[:, :, :, 0]
     threshdata = (pdata > 0.95)*tdata
     threshimg = nibabel.Nifti1Image(np.nan_to_num(threshdata), affine=timg.affine)
+    thresimg_file = threshimg.to_filename('./img/' + study + '_consensus_t_thresholded.nii.gz')
 
     pmap_neg = os.path.join('img', study + '_consensus_1-fdr_neg.nii.gz')
     tmap_neg = os.path.join('img', study + '_consensus_t_neg.nii.gz')
@@ -180,6 +181,7 @@ def consensus_analysis(t_stat_maps, N, study,  max_activation, x_coords, y_coord
     tdata_neg = timg_neg.get_fdata()[:, :, :, 0]
     threshdata_neg = (pdata_neg > 0.95)*tdata_neg
     threshimg_neg = nibabel.Nifti1Image(np.nan_to_num(threshdata_neg), affine=timg_neg.affine)
+    threshimg_neg_file = threshimg_neg.to_filename('./img/' + study + '_consensus_t_neg_thresholded.nii.gz')
 
 
     # Combine activations and deactivations in a single image 

diff --git a/figures/lib/download_data.py b/figures/lib/download_data.py
@@ -100,6 +100,16 @@ def download_data(nv_collection, study, output_dir):
             # ds120 uses F-stats no T-stats
             (('Positive_clustered_t_stat.nii.gz', 'afni_exc_set_pos.nii.gz'),) +
             (('3dMEMA_result_t_stat_masked.nii.gz', 'afni_stat.nii.gz'),))
+        if study not in ('ds109'):
+            # We also need to download the 'old' results for ds001
+            afni_images = (
+                afni_images +
+                # There is no deactivations in ds120 with AFNI
+                (('Negative_clustered_t_stat_1.nii.gz', 'old_afni_exc_set_neg.nii.gz'),) +
+                # ds120 uses F-stats no T-stats
+                (('Positive_clustered_t_stat_1.nii.gz', 'old_afni_exc_set_pos.nii.gz'),) +
+                (('3dMEMA_result_t_stat_masked_1.nii.gz', 'old_afni_stat.nii.gz'),) +
+                (('mask_1.nii.gz', 'old_afni_mask.nii.gz'),))
     else:
         # ds120 uses F-stats no T-stats
         afni_images = (
@@ -143,6 +153,18 @@ def download_data(nv_collection, study, output_dir):
             ('05FWECorrected_OneSampT_pos_exc_set_6.nii.gz', 'fsl_spm_subject_level_perm_exc_set_pos.nii.gz'),
             ('05FWECorrected_OneSampT_neg_exc_set_6.nii.gz', 'fsl_spm_subject_level_perm_exc_set_neg.nii.gz'),
         )
+        if study not in ('ds109'):
+            # Download 'old' ds001 results
+            perm_images = ( perm_images +
+                (('perm_ttest++_Clustsim_result_t_stat_masked_1.nii.gz', 'old_afni_perm.nii.gz'),) +
+                (('perm_Positive_clustered_t_stat_1.nii.gz', 'old_afni_perm_exc_set_pos.nii.gz'),) +
+                (('perm_Negative_clustered_t_stat_1.nii.gz', 'old_afni_perm_exc_set_neg.nii.gz'),) +
+                (('OneSampT_tstat1_7.nii.gz', 'old_fsl_perm.nii.gz'),) +
+                (('05FWECorrected_OneSampT_pos_exc_set_7.nii.gz', 'old_fsl_perm_exc_set_pos.nii.gz'),) +
+                (('05FWECorrected_OneSampT_neg_exc_set_7.nii.gz', 'old_fsl_perm_exc_set_neg.nii.gz'),) +
+                (('snpmT%2B_1.nii.gz', 'old_spm_perm.nii.gz'),) +
+                (('SnPM_pos_filtered_1.nii.gz', 'old_spm_perm_exc_set_pos.nii.gz'),) +
+                (('SnPM_neg_filtered_1.nii.gz', 'old_spm_perm_exc_set_neg.nii.gz'),))
     else:
         # No permutation analyses for ds120
         perm_images = ()
@@ -173,6 +195,7 @@ def download_data(nv_collection, study, output_dir):
 
         to_download = (
             afni_images + perm_images)
+        print(to_download)
 
     for image, local_name in to_download:
         url = "http://neurovault.org/media/images/" + nv_collection + '/' + image