arthursw / automatic_lesion_detection_tool_evaluation

https://arthursw.github.io/automatic_lesion_detection_tool_evaluation/

Evaluation tool

A nice tool to evaluate the benefits of using an automatic lesion detection tool.

Usage

User interfaces

The mouse enables to navigate in the image (click and drag on the different slices), as the arrow keys and the Page Up / Page Down keys.

To zoom in and out, click and drag up or down with the ALT key pressed.

The "Toggle side view" button enables to choose between a side-to-side view and a single view. The image checkboxes enable to show / hide each image.

The "< Prev" and "Next >" buttons enable to navigate in the patient list.

Papaya shortcuts (help menu > show keyboard reference):

[Spacebar] Cycle the main slice view in a clockwise rotation.
[Page Up] or ['] Increment the axial slice.
[Page Down] or [/] Decrement the axial slice.
[Arrow Up] and [Arrow Down] Increment/decrement the coronal slice.
[Arrow Right] and [Arrow Left] Increment/decrement the sagittal slice.
[g] and [v] Increment/decrement main slice.
[<] or [,] Decrement the series point.
[>] or [.] Increment the series point.
[o] Navigate viewer to the image origin.
[c] Navigate viewer to the center of the image.
[a] Toggle main crosshairs on/off.

Create a task file to view a database

The task folder structure must be the following:

/path/to/session1
├── patient1
│   ├── clinical_case.txt
│   ├── flair1.nii.gz
│   ├── flair2.nii.gz
│   ├── report.pdf
│   └── segmentation.nii.gz
├── patient2
│   ├── ...

The create_patient_list.py script in this repository is an example to create a json task file.

A task file has the following structure:

{
	{
	"patients": [
		{
			"name": "patient01", 															# The patient name
			"description": "Patient: 8099YL-GMMZZO-0417OF-RMMMVC, patient: 5", 				# The patient description
			"images": [																		# The image list for this patient
				{
					"name": "time01",														# The name of the image
					"file": "8099YL-GMMZZO-0417OF-RMMMVC_flair_time01.nii.gz",				# The path of the image in the image archive or folder
					"parameters": {															# The [Papaya images options](https://github.com/rii-mango/Papaya/wiki/Configuration#image-options))
						"minPercent": 0,													# Can be min or minPercent
						"maxPercent": 1,													# Can be max or maxPercent, a nice trick is to use different max values on the same look-up table to display different label images with different colors
						"lut": "Grayscale"
					},
					"display": true 														# Wether to display the image by default or not
				},
				{
					"name": "time02",
					"file": "8099YL-GMMZZO-0417OF-RMMMVC_flair_time02.nii.gz",
					"parameters": {
						"minPercent": 0,
						"maxPercent": 1,
						"lut": "Grayscale"
					},
					"display": true
				},
				[...]
			]
		},
		[...]
	],
	"fields": [																				# The list of the custom fields in the patient table
		{
			"field": "new",																	# The field name
			"sortable": true,																# The column will be sortable
			"resizable": true,																# The column (width) will be resizable
			"filter": true,																	# Enable to filter the column
			"editable": true,																# Enable to edit values in the column
			"longiseg_type": "bool",														# Create a checkbox in the column for this boolean value
		},
		{
			"field": "growing",
			"sortable": true,
			"resizable": true,
			"filter": true,
			"editable": true,
			"longiseg_type": "bool",
		}
	]
}
}

The image archive or folder is just the place containing all images refered in the "images" attributes of the patients of a task. In the example above, the images folder must at least contain the images 8099YL-GMMZZO-0417OF-RMMMVC_flair_time01.nii.gz and 8099YL-GMMZZO-0417OF-RMMMVC_flair_time02.nii.gz. It can also contains other files.