Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
Function 1: Single perfusion inter-patient PCA.
Also this should not require the -t parameter as there is no testing for this function.
$ PerfusionPCA -i input_singlesubject -n 3 -o output_singlesubject
The required parameter 't' is missing from the command line arguments you provided. See 'PerfusionPCA --help' for extended help.
$ PerfusionPCA -i input_singlesubject -n 3 -o output_singlesubject -t 0
Input File:input_singlesubject
Output Directory:output_singlesubject
There is no subject with the required input in the given directory.
Function2-1: Multi-subject Intra-subject PCA
Preparing a model. This should not require a -n
$ PerfusionPCA -i input_multisubject -o output_singlesubject -t 0
The required parameter 'n' is missing from the command line arguments you provided. See 'PerfusionPCA --help' for extended help.
$ PerfusionPCA -i input_multisubject -o output_singlesubject -t 0 -n 45
Input File:input_multisubject
Output Directory:output_singlesubject
There is no subject with the required input in the given directory.
Expected Behavior
Functionality 1: Obtain Intra-subject PCA for a single perfusion input
User input - one 4D perfusion image, 3D ROI mask(s), number of PCA components (N), and output directory.
Output - N number of 3D images, PCA matrix, Mean csv, Variance csv
Functionality 2-1: Obtain Inter-patient PCA, Prepare a model based on multiple subjects
User input – Directory that includes a collection of perfusion image and ROI mask per subject; output directory of model
Output – PCA matrix, Mean csv, Variance csv
Functionality 2-2: Obtain Inter-patient PCA, Apply the model prepared in 2-1 to a new image
Input – 4D perfusion image, N, output directory, and model directory (output of Functionality 2 )
Output – N number of 3D images
CaPTk Version
1.8.0.Beta on cluster
Desktop (please complete the following information):
cbica-cluster
Describe the bug PerfusionPCA application doesn't produce output
To Reproduce Files are in
Function 1: Single perfusion inter-patient PCA. Also this should not require the -t parameter as there is no testing for this function.
Function2-1: Multi-subject Intra-subject PCA Preparing a model. This should not require a -n
Expected Behavior
Functionality 1: Obtain Intra-subject PCA for a single perfusion input
Functionality 2-1: Obtain Inter-patient PCA, Prepare a model based on multiple subjects
Functionality 2-2: Obtain Inter-patient PCA, Apply the model prepared in 2-1 to a new image
CaPTk Version 1.8.0.Beta on cluster
Desktop (please complete the following information): cbica-cluster