Volumetry outputs are provided in comma-separated-values files (extension .csv).
These files are encoded in ASCII and can be viewed through datasheet editors such as Excel or Google Sheets, or directly through any text editor, where commas separate the values from one field to the next.
Output values are exported as a multi-column document, where each column corresponds to a specific field or type of value.
The first row indicates the names of each corresponding fields.
This document covers the most extensive results case. Depending on the morphometric tool used and the advanced settings selected, some fields might not appear or have 0/nan values.
Column fields:
- Region name (label)
This is the label name for the tissue type or region corresponding to that row, the data of every other column over the same row will relate to this region. - Centroid coordinates (x, y, z)
The first three columns, x, y, z define the coordinates for the geometric centre, or centroid, of the region or tissue corresponding to that row. It is calculated by averaging the coordinates of all voxels belonging to that tissue/region.
Derived measures such as intra-cranial volume (ICV) or brain parenchymal fraction (BPF) have 0-values in these fields. - Label-value (value)
This is the label-identification numerical value that voxels belonging to the corresponding tissue/region have in the tissue-segmentation or label images.
Derived measures such as ICV or BPF have 0-values in these fields. - Voxel count (count)
Represents the number of voxels belonging to the corresponding tissue/volume. - Tissue/Region volume (volume)
This value shows the actual volume in mm3 of the corresponding tissue/region, it is calculated by multiplying the voxel count by the volume of a single voxel given the data resolution. In the case of Freesurfer analysis, this value is obtained directly from the script and uses surface computation information to calculate volumes. - Label group (group)
The value in this field indicates to which label group the current region belongs to.
For tissue types, this field contains the same text as the region name.
For atlas-based parcellated regions, they can belong to one of 5 possible groups: left (hemisphere), right (hemisphere), Subcortical-Left, Subcortical-Right, and Brainstem. - Cortical thickness average value (thick_avg)
This field contains the average of all cortical thickness measurements obtained within the defined region.
This field may not be present in tissue segmentation outputs files.
This field only related to cortical regions. When present, tissue type regions, and sub-cortical regions will have 0-values in this field. - Cortical thickness standard deviation (thick_std)
This field contains the standard deviation of all cortical thickness measurements obtained within the defined region.
This field may not be present in tissue segmentation outputs files.This field is only related to cortical regions. When present, tissue type regions, and sub-cortical regions will have 0-values in this field.
Regions:
- Tissue types
These refer to the volumes obtained during tissue segmentation:- CSF: cerebrospinal fluid.
- Gray matter: depending on the atlas scheme used, this might refer to whole brain gray matter, or only to cortical brain matter.
- Deep brain: subcortical gray-matter.
If the atlas scheme used does not provide deep brain priors, the values in this row will be zero, and Gray matter will refer to whole brain gray matter.
Otherwise, the "Gray matter" row will refer to only cortical brain matter. - White matter
- Brain-stem: values might be 0 if the atlas scheme used does not provide brain-stem priors.
- Cerebellum: values might be 0 if the atlas scheme used does not provide cerebellum priors.
- ICV: intracranial volume
consists of the sum of all previous tissue types, and can be used to normalize tissue/region volume values, so that they can be compared across subjects, by eliminating the possible bias of absolute head size. - BPF: brain parenchymal fraction (%)
It is the ratio of brain parenchymal volume to the total volume within the brain surface contour, that is, the ratio of the sum of all tissue types except CSF to the ICV.
It's evolution over time is commonly used as a measure of brain atrophy.
- Atlas-derived
These are regions as defined by the atlas scheme (i.e: DKT40 or LPBA40).
In some cases, these regions might not be found in the subject and the related fields will have 0/nan values.
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