Merge branch 'devel' of github.com:layerfMRI/LAYNII into devel

layerfMRI · Sep 12, 2021 · 2b88ba6 · 2b88ba6
2 parents 1545f1a + b1c6cea
commit 2b88ba6
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/src/LN2_MASK.cpp b/src/LN2_MASK.cpp
@@ -35,7 +35,7 @@ int show_help(void) {
     "\n"
     "Notes:\n"
     "    - This refers to layerfMRI artifact here: \n"
-    "        TODO: <add link here>\n"
+    "        https://twitter.com/layerfMRI/status/1375067409523093513\n"
     "    - Note that columns and scores are expected to be positive numbers \n"
     "\n");
     return 0;

diff --git a/src/LN2_PATCH_FLATTEN.cpp b/src/LN2_PATCH_FLATTEN.cpp
@@ -200,7 +200,7 @@ int main(int argc, char*  argv[]) {
 
     // ========================================================================
     // Prepare outputs
-    nifti_image* out_cells = copy_nifti_as_int32(nii_input);
+    nifti_image* out_cells = copy_nifti_as_int32(domain);
     int32_t* out_cells_data = static_cast<int32_t*>(out_cells->data);
 
     for (int i = 0; i != nr_voxels; ++i) {
@@ -332,7 +332,7 @@ int main(int argc, char*  argv[]) {
         int k = cell_idx_d * nr_cells + j;
 
         // Write cell index to output
-        *(out_cells_data + i) = j;
+        *(out_cells_data + i) = j + 1;
 
         // Write visited voxel value to flat cell
         *(flat_values_data + k) += *(nii_input_data + i);
@@ -341,7 +341,11 @@ int main(int argc, char*  argv[]) {
         *(flat_domain_data + k) += *(domain_data + i);
     }
 
-    save_output_nifti(fout, "UV_cells", out_cells, true);
+    // Add bin dimmensions into the output tag
+    std::ostringstream tag_u, tag_v;
+    tag_u << bins_u;
+    tag_v << bins_v;
+    save_output_nifti(fout, "UV_cells"+tag_u.str()+"x"+tag_v.str(), out_cells, true);
 
     // Take the mean of each projected cell value
     for (int i = 0; i != nr_bins; ++i) {