User-Defined Atlases

It is possible for users to prepare their own VOI atlases for use in PNEURO. Note, however, that they are only applicable for Maximum Probability Atlas approach, not for the Brain Parcellation approach.

The following sets of data are need to be prepared for a user-defined atlas:

Atlas image: Image which encodes the atlas VOIs as numeric labels.
Label list: Text file mapping the label values to VOI names.
Manifest: Text file for the defining of the species type
Normalization files for calculating the transformation between the subject anatomy and atlas anatomy.

This information has to be organized in a subdirectory of resources/templates/voitemplates in a particular way as illustrated below.

AAL Template Organization

The atlas name (e.g. AAL-Merged) has to be used as the name of the sub-directory, the atlas image (AAL-Merged.nii), the label list (AAL-Merged.txt), and the manifest (AAL-Merged.manifest).

Atlas Image

The atlas image must be prepared as a NifTI file and encode the atlas VOIs as numeric labels. Each pixel has a value of 0 if it is a background pixel, or otherwise an integer number. We recommend using the HFS anatomical orientation (head first, supine = radiological convention) for human data.

Label List

The label list text file has the minimal form:
name1 outlined_name1 label_value1
name2 outlined_name2 label_value2
where each VOI is represented by a line.

The list can be extended with additional information for the VOI presentation as illustrated below for the AAL-Merged.txt. The first column starts with the name followed by a bracket construction which encodes a tree structure. For instance, Precentral belongs to the Frontal_Lobe which is located in the left L or right R hemisphere. The second column indicates the name of a generated contour VOI. The third column contains the label value in the atlas file. Each pixel in AAL-Merged.nii with value 1 will belong the Precentral_l VOI, pixels with value 2 to Precentral_l, etc. The third column specifies the RGB color values for showing the VOI, and the last column the text to be shown as a tooltip.

The corresponding atlas VOI structure is illustrated below.

There are additional options to be added in the columns:

E: Excluded from masking by the grey matter threshold.
O: Indicates that the VOI is not brain matter.
H: Indicates that the VOI should initially be hidden, i.e. not selected on the Group panel.
L, R: Indicates that the VOI belongs to the left (L) or right (R) hemisphere. This information is used in sulci deformation.
C: Indicates that the VOI belongs to the cerebellum. This information is used in sulci deformation.

Example as shown in Excel:

Normalization Files

Atlases can only be applied to images if they have the same resolution and show the anatomy with the same geometry. Therefore, images originating from real experiments first need a normalization step for the atlas to be applied. This is done by calculating a normalization transform between the subject image and a "template" image representing the standard anatomy imaged with a certain modality, and using it for warping the VOIs to the subject anatomy.

Appropriate template images need to be copied to a normalization sub-folder. In the example below normalization contains T1 and T2 MR templates with and without skull, as well as a PET template. All of these templates show the anatomy in the MNI space in which the AAL VOIs were defined.

The normalization works best if the information is restricted to the relevant image part. Therefore, normalization should contain a mask sub-folder with a mask file brainmask.nii containing 1 for all relevant pixels and 0 for all others.