add N4 option to specify number of resolutions and iterations

ayendiki · Sep 19, 2020 · f5d43e9 · f5d43e9
1 parent dcf4971
commit f5d43e9
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Showing 2 changed files with 15 additions and 9 deletions.
diff --git a/AntsN4BiasFieldCorrectionFs/AntsN4BiasFieldCorrectionFs.cpp b/AntsN4BiasFieldCorrectionFs/AntsN4BiasFieldCorrectionFs.cpp
@@ -33,6 +33,7 @@ int main(int argc, char **argv)
   parser.addArgument("-i", "--input",  1, String, true);
   parser.addArgument("-o", "--output", 1, String, true);
   parser.addArgument("-s", "--shrink", 1, Int, false);
+  parser.addArgument("-t", "--iters", '+', Int, false);
   parser.parse(argc, argv);
 
   std::string inputname = parser.retrieve<std::string>("input");
@@ -60,10 +61,13 @@ int main(int argc, char **argv)
   CorrecterType::Pointer correcter = CorrecterType::New();
 
   // convergence options
-  CorrecterType::VariableSizeArrayType maximumNumberOfIterations(4);
-  maximumNumberOfIterations.Fill(50);
+  // set number of iterations (default is 50x50x50x50)
+  std::vector<int> numIters = {50, 50, 50, 50};
+  if (parser.exists("iters")) numIters = parser.retrieve<std::vector<int>>("iters");
+  CorrecterType::VariableSizeArrayType maximumNumberOfIterations(numIters.size());
+  for (unsigned int d = 0; d < numIters.size(); d++) maximumNumberOfIterations[d] = numIters[d];
   correcter->SetMaximumNumberOfIterations(maximumNumberOfIterations);
-  correcter->SetNumberOfFittingLevels(4);
+  correcter->SetNumberOfFittingLevels(numIters.size());
   correcter->SetConvergenceThreshold(0.0);
 
   // shrink the image to save time

diff --git a/AntsN4BiasFieldCorrectionFs/AntsN4BiasFieldCorrectionFs.help.xml b/AntsN4BiasFieldCorrectionFs/AntsN4BiasFieldCorrectionFs.help.xml
@@ -4,14 +4,16 @@
   <description>Runs N4 (nonparameteric, nonuniform normalization) retrospective bias correction on an image. This programs wraps the AntsN4BiasFieldCorrection utility available in the ANTs package (see http://stnava.github.io/ANTs).</description>
   <arguments>
     <required-flagged>
-      <argument>-i, --input invol</argument>
-      <explanation>input volume file</explanation>
-      <argument>-o, --output outvol</argument>
-      <explanation>corrected volume file</explanation>
+      <argument>-i, --input FILE</argument>
+      <explanation>Input volume file.</explanation>
+      <argument>-o, --output FILE</argument>
+      <explanation>Corrected volume file.</explanation>
     </required-flagged>
     <optional-flagged>
-      <argument>--shrink</argument>
-      <explanation>resample factor to decrease computation time (default is 4)</explanation>
+      <argument>-s, --shrink INT</argument>
+      <explanation>Resample factor to decrease computation time. Default is 4.</explanation>
+      <argument>-t, --iters INT [INT...]</argument>
+      <explanation>Number of resolutions and max iterations per resolution. Default is `50 50 50 50`, which indicates 4 fitting levels with 50 iterations each.</explanation>
     </optional-flagged>
   </arguments>
 </help>