Create 3D surfaces using Mango

Mango (http://ric.uthscsa.edu/mango/) is a useful tool for creating 3D surfaces from label files. This can be helpful in displaying the spatial organization of a label/region of interest, especially in comparison to a slice view. To do this, you will need to convert your label to a nifti file, create a separate file for each label value, then create a surface for each of these files using mango. Instructions and examples are below.

In the instructions below, left-hc.mnc is the original label file. It has 4 values (1, 2, 3, 4).

1. Convert .mnc to .nii Fix the range of the .mnc file, this ensures label values don’t get distorted in the conversion. Without this, you could have label 1 end up with a value of 1.005 for example. The following mincreshape command does this:

module load minc-toolkit
mincreshape -normalize -unsigned -byte -image_range 0 255 -valid_range 0 255 left-hc.mnc left-hc_fix.mnc

Convert to .nii, zip the file

mnc2nii left-hc_fix.mnc left-hc_fix.nii
gzip left-hc_fix.nii

2. Separate the file such that you have one file for each label value (4 total files in this example). You can use the fslmaths command to do this as follows:

module unload minc-toolkit
module load FSL
fslmaths left-hc_fix.nii.gz -thr 1 -uthr 1 left-hc_fix_1.nii.gz
fslmaths left-hc_fix.nii.gz -thr 2 -uthr 2 left-hc_fix_2.nii.gz
fslmaths left-hc_fix.nii.gz -thr 3 -uthr 3 left-hc_fix_3.nii.gz
fslmaths left-hc_fix.nii.gz -thr 4 -uthr 4 left-hc_fix_4.nii.gz

Use fsleyes to view each of the created files above to ensure they are as expected:

fsleyes left-hc_fix_1.nii.gz

3. Use mango to create a surface for each of the separate label files. You can open mango from the command line by running the command mango

module load mango
mango

4. Open the first of your label files using the Open tab:

5. Under the Image tab, select build surface:

Click ok, and mango will build a surface. This may take up to a minute. After the surface is complete, a new window will pop up displaying the newly created surface.

6. In the surface window, use the File tab to export the surface as a .vtk file:

7. After exporting, close the image window. Then repeat steps 4-6 for each label value. After creating a surface for your final label, build the surface and export to a .vtk file. Instead of closing the surface and image windows, load in the other surfaces you created using the Shapes -> load from file tab:

You should then be able to view all of your newly created surfaces together.

8. For visualization purposes, you can change the colour of each surface by using the 'Material' option: