Input Ground Truth

The input ground truth, known as the High Resolution Ground Truth (or HRGT) comprises of a 5-dimensional NIFTI image, and json parameter file that describes the NIFTI and also supplies any non-image ground truth parameters. 3D Volumes for each ground truth quantity are concatenated along the 5th NIFTI dimension.

../_images/ground_truth_concatenation.png

Different HRGT’s are selected by modifiying the “ground_truth” entry in the input parameter file to the name of the ground truth being used. For example:

{
    "global_configuration": {
        "ground_truth": "hrgt_icbm_2009a_nls_3t"
    },
    ...
}

will use the built-in ground truth “hrgt_icbm_2009a_nls_3t” (see below for more details of these datasets). In addition, it is possible to specify your own ground truth files by using one of the following:

{
    "global_configuration": {
        "ground_truth": "/path/to/nifti_file.nii"
    },
    ...
}

or:

{
    "global_configuration": {
        "ground_truth": {
            "nii": "/path/to/nifti_file.nii.gz"},
            "json": "/path/to/json_file.json"}
    },
    ...
}

In the two examples above, the first example assumes there is a JSON file at precisely the same path with the same filename, except for a ‘.json’ extension instead of a ‘.nii’/’.nii.gz’ extension. The second example uses an explicitly defined filename for each file type, and may have different paths.

Custom ground truth

To make your own input ground truth please see Making an input ground truth

Augmenting values

HRGT parameters and image values can be augmented using the input parameter file. See Parameters for more information. ASLDRO currently supports the following built-in ground truths:

hrgt_icbm_2009a_nls_3t

Normal adult 3T ground truth. A 1x1x1mm ground truth based on the MNI ICBM 2009a Nonlinear Symmetric template, obtained from http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009, with quantitative parameters set based on supplied masks. This ground truth has the following values for each tissue and quantity (corresponding to 3T):

Tissue

Perfusion Rate [ml/100g/min]

Transit Time [s]

T1 [s]

T2 [s]

T2* [s]

label

Grey Matter

60.00

0.80

1.330

0.080

0.066

1

White Matter

20.00

1.20

0.830

0.110

0.053

2

CSF

0.00

1000.0

3.000

0.300

0.200

3

label is the integer value assigned to the tissue in the seg_label volume.

hrgt_icbm_2009a_nls_1.5t

Normal adult 1.5T ground truth. A 1x1x1mm ground truth based on the MNI ICBM 2009a Nonlinear Symmetric template, obtained from http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009, with quantitative parameters set based on supplied masks. This ground truth has the following values for each tissue and quantity (corresponding to 1.5T):

Tissue

Perfusion Rate [ml/100g/min]

Transit Time [s]

T1 [s]

T2 [s]

T2* [s]

label

Grey Matter

60.00

0.80

1.100

0.092

0.084

1

White Matter

20.00

1.20

0.560

0.082

0.066

2

CSF

0.00

1000.0

3.000

0.400

0.300

3

label is the integer value assigned to the tissue in the seg_label volume.