Modify Perfusion Derivatives documentation

[ashishsingh18]

Describe the bug Modify Perfusion Derivatives documentation in html and on the CLI as per @chiharusako's suggestions below.

in HTML:

This application extracts various measurements from a Dynamic-Susceptibility Contrast-enhanced (DSC) MRI scan. This application is also available from the web on the CBICA Image Processing Portal. Please see the experiment on the portal for details. The extracted measurements comprise of the following:

1. An automatically-extracted proxy to relative Cerebral Blood Volume (ap-rCBV)
2. Peak Height (PH)
3. Percentage Signal Recovery (PSR) By default, all calculations use the average of the first 20% of timepoints as baseline, and the average of 66-88% timepoints as recovery. The timepoint with the maximum intensity drop on the average curve must fall between the baseline and recovery time ranges. Optional percentage time ranges can be applied in the CLI if the default needs to be changed. Note: The ap-rCBV measurement is not expected to be identical to the clinically extracted rCBV measurement.

REQUIREMENTS:

1. A single DSC-MRI image with non-negative values.
2. System should have at least (add space) 32GB RAM for calculating perfusion derivatives (This is not a general requirement - This is true if the perfusion file is resampled and very big, but original perfusion files are usually smaller and can calculate with less RAM…)
3. Output directory
4. [OPTIONAL] The baseline start threshold percentage (range[0-100], Default = 0)
5. [OPTIONAL] The baseline end threshold percentage (range[0-100], Default = 20)
6. [OPTIONAL] The recovery start threshold percentage (range[0-100], Default = 66)
7. [OPTIONAL] The recovery end threshold percentage (range[0-100], Default = 88) USAGE:
8. Launch the application from "Applications" -> "Perfusion Derivatives".
9. Specify the input DSC-MRI image, the perfusion measurements (i.e., ap-rCBV, PH, PSR) to be extracted, the "Echo Time" of the loaded scan in seconds (45 milliseconds = 0.045 seconds), and the output directory. Echo Time is no longer an input. Please check that it’s not an input in GUI as well!
10. Press the "Confirm" button.
11. The extracted measurements will be saved at the specified location (~5 minutes). ${CaPTk_InstallDir}/bin/PerfusionDerivatives.exe -i C:/InputImage/convertedNIfTIPerf_image.nii.gz -p 1 -r 1 -o C:/OutputDir

[ashishsingh18]

And on the CLI:

Description:

Perfusion Derivatives calculation based on specific parameters

Usage:

:::Required parameters:::

[ -i, --input] The input DSC-MRI image. Expected Type :: STRING Expected Range ::

[ -o, --output] The output directory. Expected Type :: STRING Expected Range ::

:::Optional parameters:::

[ -u, --usage] Prints basic usage message

[ -h, --help] Prints verbose usage information

[ -v, --version] Prints information about software version

[ -rt, --runtest] Runs the tests

[-cwl, --cwl] Generates a .cwl file for the software

[ -bs, --baseline start] The baseline start threshold percentage (range[0-100], Default = 0) Expected Type :: FLOAT Expected Range ::

[ -be, --baseline end] The baseline end threshold percentage (range[0-100], Default = 20) Expected Type :: FLOAT Expected Range ::

[ -rs, --recovery start] The recovery start threshold percentage (range[0-100], Default = 66) Expected Type :: FLOAT Expected Range ::

[ -re, --recovery end] The recovery end threshold percentage (range[0-100], Default = 88) Expected Type :: FLOAT Expected Range ::

[ -p, --PSR] Output the Percentage Signal Recovery image (1=YES, 0=NO, 1 (Default)) Expected Type :: STRING Expected Range ::

[ -pH, --peakHeight] Output the Peak Height image (1=YES, 0=NO, 1 (Default)) Expected Type :: STRING Expected Range ::

[ -r, --apRCBV] Output the Automatially-extracted proxy to reletive cerebral volume image (1=YES, 0=NO, 1 (Default)) Expected Type :: STRING Expected Range ::

[ -L, --Logger] Full path to log file to store console outputs By default, only console output is generated Expected Type :: STRING Expected Range :: log file which user has write access to

Examples of Usage:

Command: PerfusionDerivatives.exe -i input_image.nii.gz -o

Result : Calculates the perfusion derivates of the input image