Merge pull request #3 from niivue/hollow

Hollow

Author: neurolabusc

README.md

@@ -12,7 +12,8 @@ This is an extension of [brainchop](https://github.com/neuroneural/brainchop) th
 4. **Option 3** If your image is in DICOM format, it may load if you drag and drop the files. If this fails, convert your images with [dcm2niix](https://niivue.github.io/niivue-dcm2niix/) and save the result as a NIfTI format file that brain2print can open.
 5. Segment your brain scan by choosing a model from the `Segmentation Model` pull-down menu. Not all models work with all graphics cards. The `Tissue GWM (High Acc, Low Mem)` is a good starting point. Hopefully, it will accurately segment your brain into gray matter, white matter and cerebral spinal fluid.
 6. Press the `Create Mesh` button and select your preferred settings:
-  - ![settings dialog](Settings.png)
+  - ![settings dialog](preferences.png)
+  - The `Hollow` option allows you to choose between a solid object or a surface shell (which uses less material to print).
   - You can choose `Smoothing` to make the surfaces less jagged at the expense of computation time.
   - You can choose to `Simplify` to reduce the number of triangles and create smaller files.
 7. Once you have set your preferences, press `Apply`.
@@ -42,6 +43,7 @@ npm run build
 
 This web page combines three packages developed by our team:
 
-- [brainchop](https://github.com/neuroneural/brainchop) AI models for tissue segmentation.
-- [niivue](https://github.com/niivue/niivue) reading images and visualization
-- [ITK-Wasm](https://github.com/InsightSoftwareConsortium/ITK-Wasm) for voxel-to-mesh and mesh processing
+- [brainchop](https://github.com/neuroneural/brainchop) AI models for tissue segmentation. [Citation](https://pubmed.ncbi.nlm.nih.gov/39301517/).
+- [niimath](https://github.com/rordenlab/niimath) for creating hollow objects. [Citation](https://pubmed.ncbi.nlm.nih.gov/39268148/).
+- [niivue](https://github.com/niivue/niivue) reading images and visualization.
+- [ITK-Wasm](https://github.com/InsightSoftwareConsortium/ITK-Wasm) for voxel-to-mesh and mesh processing. [Citation](https://proceedings.scipy.org/articles/TCFJ5130.

Settings.png

@@ -65,6 +65,19 @@
   </footer>
   <dialog id="remeshDialog">
     <form method="dialog">
+      <p>
+        <label>
+          Hollow:
+          <select id="hollowSelect" title="hollow meshes require less material but may be fragile">
+            <option value="0" selected>False: solid</option>
+            <option value="-1">1mm</option>
+            <option value="-2">2mm</option>
+            <option value="-4">4mm</option>
+            <option value="-8">8mm</option>
+            <option value="-16">16mm</option>
+          </select>
+        </label>
+      </p>
       <p>
         <label for="smoothSlide">Smoothing</label>
         <input
@@ -79,7 +92,7 @@
       </p>
       <p>
         <label>Simplify Percent (10..150)</label>
-        <input title="triangle reduction reduces the file size and computation time but can reduce mesh quality, smaller values result in a smaller mesh" id="shrinkPct" type="number" min="10"  value="75" max="150">
+        <input title="triangle reduction reduces the file size and computation time but can reduce mesh quality, smaller values result in a smaller mesh" id="shrinkPct" type="number" min="10"  value="25" max="150">
       </p>
       <button id="cancelBtn" formmethod="dialog">Cancel</button>
       <button autofocus id="applyBtn" value="default">Apply</button>