Usage¶

Basics¶

The trial bureau tools are accessed from command line. On windows you can start a command line (also called ‘terminal’ or ‘shell’) in the following way:

Press windows-key + r
type ‘cmd’ and press enter

After that, typing 'tbt' + enter will show the different commands available trial bureau tools.

You can add ‘–help’ to any command to see more info on using it. For example tbt sort --help

DICOM sorter¶

To sort all DICOM files in directory job1 using the nucmed pattern:

$ tbt sorter sort job1 nucmed

To see what the ‘nucmed’ pattern is exactly:

$ tbt sorter pattern list

By default, sorting /folder1 will write sorted output to /folder1_sorted. You can also set the output folder manually:

$ tbt sorter sort job1 nucmed --output_folder C:/temp/myfolder

DICOM path patterns¶

Typing tbt sorter pattern list will by default show the following:

$ tbt sorter pattern list
> idis: (0010,0020)/(0008,1030)-(0008,0050)/(0008,103e)-(0008,0060)-(0020,0011)/(count:SOPInstanceUID)
> nucmed: (0010,0020)/(0008,1030)-(0008,0050)/(0008,0020)/(0008,103e)-(0008,0060)-(0020,0011)/(count:SOPInstanceUID)

These are the DICOM path patterns. These are text strings consisting of any combination of the following elements:

Element	Examples	Description
Text	`Folder` `file-` `/tmp`. `.dcm`	Just any free text, inc. slash and -
Dicom Tag Code	`(0010,0020)` `(0008,103e)`	A dicom tag with colons around it
Dicom Tag Name	`(PatientID)` `(SopInstanceUID)`	A dicom tag name
count: marker	`(count:PatientID)` `(count:0008,103e)`	Will number the given tag

To see a list of available Dicom tag codes and names, use tbt sorter pattern list_dicomtags

Dicom Pattern resolution¶

For each DICOM file a new path will be created by reading its values and filling in the pattern. For example, for a file with PatientID ‘1234’ and SopInstanceUID ‘1.1.1’:

Pattern	Result (1 file)
`/folder1/(PatientID)/(SopInstanceUID).dcm`	`/folder1/1234/1.1.1.dcm`

Counting¶

Counting can be useful to make paths shorter. By adding count: to an element, the sorter will number each unique value. For example, for three files with the same PatientID but separate SopInstanceUIDs:

Pattern without :count	Result (3 files)
`/folder1/(PatientID)/(SopInstanceUID).dcm`	`/folder1/1234/1.3451.35356.4234.1.dcm`
	`/folder1/1234/1.3451.35356.4234.2.dcm`
	`/folder1/1234/1.3451.35356.4234.3.dcm`

Pattern with :count	Result (3 files)
`/folder1/(PatientID)/file(count:SopInstanceUID).dcm`	`/folder1/1234/file0.dcm`
	`/folder1/1234/file1.dcm`
	`/folder1/1234/file2.dcm`

Adding custom patterns¶

To add a new pattern /folder1/(PatientID)/file(count:SopInstanceUID).dcm named test:

$ tbt sorter pattern add test /folder1/(PatientID)/file(count:SopInstanceUID).dcm

To remove this pattern again:

$ tbt sorter pattern remove test