Image Analysis Applications

Several Image analysis applications are available on the system for the analysis of chest and cardiac CT images. All of these applications have the same user interface as described below

Syntax:

                  <application>   [if=]<input>  [of=]output [od=<output-directory>] [-ic] [-csv]

Description:

The program with the name <application>  is run on a set of images specified by the <input> list and returns the <output> a csv file of the results, one row per image. All the output values created by the application are returned in the output csv file.  In some cases, multiple output rows are generated for each image. For example, the nodule detection algorithms produce one row for each detected lung nodule.

Options:

if=<file>The list of images specified by image-codes to be processed. One image-code per line. Two other input formats are possible as determined by option settings.

of=<file> The file name of the csv result file

od=<directory> All outputs form the application (especially processed intermediate images),  may be optionally saved when the od= option is specified. The result for each image is saved in a directory which has the name of the image-code inside the <directory> specified by od=.

-ic          The input (if=) specifies a single image-code that is to be analyzed

-csv       The input list is specified by a csv file with a column labeled “image” that contains the image-codes to be processed.

 

Currently the following applications are available:

vsybil	Runs the Sybil lung cancer analysis program. The predictions for the next five years are output
vmonodule	This application runs the MONAI lung nodule detection algorithm
vtsnodule	Runs the TotalSegmentator (Bluemind) nodule detection algorithm
vdcmtags	Reports a set of DICOM tag values for each image
See Also
vprogress	When given the image-list and output.csv file names for a currently running analysis, it will print what fraction of the images have been processed and what is the name of the most recently processed image.
ldocker	runs any of the installed HL Dockers with the same command line syntax. The current HL analysis function  are:   ·      Bone mineral density, ·      Heart chambers, ·      Fat, ·      Liver ·      Emphysema