Structure of VOI Atlases in PMOD

A VOI atlas in PMOD consists of the following components:

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 (HUMAN, PRIMATE, PIG, RAT, MOUSE) by a simple line entry, e.g.
SPECIES = HUMAN
If the VOI atlas is not applicable in PNEURO then the line
APPLICATION = NO_PNEURO
should be added. For probabilistic atlases the line
TYPE = PROBABILISTIC, RANGE 0 / 100
The range specified for the data will be scaled to a probability value in the range [0,1].
The space definition is applicable only for the human species.

SPACE = MNI
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).

By conforming to this structure it is possible for users to prepare their own VOI atlases. PNEURO supports user define atlases for both Maximum Probability Atlas approach and for the Brain Parcellation approach.

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 Left or right Right_hemisphere of the Cerebral_cortex. 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 belongs to the Precentral_l VOI, pixels with value 2 to Precentral_r, 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.

Note:

The list structure has to be homogeneous: similar type of information has to be provided for each entry in the list.

The spaces in the Name field are not allowed.

The corresponding atlas VOI structure is illustrated below.

There are additional options to be added in the columns for use in PNEURO:

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 also used in sulci deformation.

Example as shown in Excel:

Spatial Normalization

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.

Name of method in PMOD	Methodology and template
Template-based normalization	Implementation of the spatial normalization in SPM5. It requires a template image in the atlas space which has a similar pattern as the image to normalize. The usual reference images are the PET, T1 and T2 SPM5 templates.
3 Probability maps normalization	Implementation of the unified segmentation normalization in SPM8. It requires tissue probability maps of grey matter, white matter and CSF in the atlas space, which is organized in a dynamic file called tpm.nii. This normalization is mostly applicable to T₁-weighted MR images.
6 Probability maps normalization	Implementation of the unified segmentation normalization in SPM12. It uses three additional probability maps (bone, tissue and air), which are organized in a dynamic file tpm_6.nii.

Template Normalization Files

Appropriate template images for the Template-based normalization (SPM5) 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.

UserDefineAtlas_NormalizationFolderContent

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 mask.nii containing 1 for all relevant pixels and 0 for all others.

The normalization folder of a user define atlas contains two templates: the T1 MR and the PET. The templates show the anatomy in the space in which the VOIs atlas was define. The atlas name (e.g. BRAIN_AAL_Merged) has to be used as the root name for the templates followed by the suffixes -MR (BRAIN_ALL_Merged-MR.nii) and -PET (BRAIN_ALL_Merged-PET.nii) for the MR and PET template respectively.

Probability Normalization Files

The normalization files for the two probability maps approaches need to be prepared in a normalization/tmp subdirectory as illustrated below.

Note: The human brain atlases for which the manifest file contains SPECIES = HUMAN and SPACE = MNI definitions do not require the preparation of the normalization subdirectory. In such cases the universal MNI files for the human brain available in the template and the tpmaps directories will be used.