Hippocampal subregions

The image on the right was created with mricron, mrcros, and Subject 1 of the Winterburn atlas.

Files are available at: https://drive.google.com/open?id=0B_EI_zLvCe3fWVNyUkJrbzlEdzA

The citation is here: https://www.ncbi.nlm.nih.gov/pubmed/23415948

3D views in MRIcroS

• Make sure Winterburn atlas labels are separated out
  • There should be files "rlabels_val00[N].nii". 
  • To create, CSPM → VOI → created with the CPM => VOI => Extract individual VOI from multi-label file
    • Select the resliced file (rT1 left/right.nii)
• After starting CSPM, edit the file "shape_manual"

>>edit shape_manual

• Set the path to the atlas subject (1)
• Edit the colors (2)

• Save and run (click green "Run" button) 

Cross sections in MRIcroN

The general approach is simple: open the anatomical, overlay the regions, and set the color scheme. Since the original T1 is at 0.3 mm³, it is very large and the whole-brain volume will not open in the standard mricron. You can use the 64-bit mricron instead. It can be interesting to view the  T1 and T2 images at this high resolution.

The practical alternative is to use an anatomical of a subsection, the "r" files. These cover the hippocampus at the same 0.3mm³ resolution, but can open in the standard 32-bit mricron.

Before starting, copy the hippocampus color scheme to mricron's library:

hippocampus.lut => C:\Program Files\mricron\lut

This will show up in the drop-down list the next time you run mricron.

• Open the rT1 (left) or rT1 (right) in mricron
• Overlay the labels
• Set the color scheme to "hippocampus"
• [[Optional]] Set overlay opacity to 0%
• Scale the overlay so that the intensity range aligns with the color scheme - see right

To edit the colors, edit the lut file in Notepad. Each row matches an intensity value to an RGB color. For example, since the Winterburn labels have five subregions on each side, there are 10 colors corresponding to the values (as in the file labels.txt).

Example of hippocampus.lut in notepad:

There are more entries at 101-106, since those are the right side values as per labels.txt.