XTOLM

XTOLM is a local bash XNAT-aware console. This documentation provides a use case for exporting data computations in XNAT to an external spreadsheet.

Read further if:

  • you develop or run image processing locally in bash shell;
  • you want to use XNAT as data source and/or remote archive;
  • you want to automate processing of multiple XNAT sessions and want to report your results in spreadsheets.
  • you want to focus on local script development and minimize programming effort to interact with XNAT.

Installing XTOLM

Client machine prerequisites to run XTOLM on a 64 bit Linux:

Make sure all required components are on your path.

XTOLM Command Reference:

Online Commands: mostly, load/save scans, resources and metadata as resources.

load_scans <id1>[,...] load scan(s) to DICOM by ID to the processing dir
load_type <type> load scan(s) DICOM of a given type to the processing dir
load_dir <dir1>[,...] load resource dir(s) to the processing dir
load_file <fil1> [fil2..] load resource file(s) to the processing dir
load_workspace load context variables from XNAT session (stored under unique analysis ID)
save_workspace

save context variables to XNAT session (stored under unique analysis ID)

save_dir <dir> write resource dir to XNAT (overwrites existing)

   

Offline Commands: The purpose is to enable repeated analysis. Each study is loaded into a separate directory and is processed within 'processing context': XNAT subject and experiment label. Each study directory can have DICOM, resource dirs, and some configuration files that store context information. Workspace is defined as all user-defined variables that should be saved as key-value pairs.

set_context <subject> <session> set current context of subject and session
save_vars [var1] [,..]  save one or more variables to current context
summary <label> generate a comma-separated summary of existing contexts
help                             list console commands
quit                             quit interactive console

Command Details

set_context: move to another processing dir that corresponds to another XNAT session, and load/init workspace variables for that session. Previously computed variables are loaded using this command.

save_vars: save local vars (name+value) to current context (context is saved in a file within processing dir or online in XNAT experiment).

load/save workspace: sync context variables with XNAT session (load/save to designated resource)

Script execution mode: the user writes a script which is interpreted by XTOLM, converted to a bash script and executed.

xtolm [options] <script file> [...]

Interactive mode : line-by-line command input.
Offline mode: all code that interacts with XNAT is ignored.
Debug mode:

Useful capabilities

rcsv: convert a csv file into a set of bash arrays - can be used in XTOLM to change session context automatically, load specific scans/dirs, etc.
summary: create a summary spreadsheet that aggregates all contexts accross the batch processing session.

XTOLM design features

  • flexible coupling with online XNAT server. The analysis can be saved/loaded from/to XNAT using unique analysis ID. However, completely offline processing is possible (-o mode), when repeated or advanced analyses are required. Context is still saved in session configuration files. The design tolerates the same script in offline mode, ignoring all local<->xnat transactions.
  • repeatability of analysis - helped by re-using saved session context. Modifying the script and re-running is easy.
  • minimal local data structure requirements.

Use case

  • Compute whole brain volume using Brain Extraction Tool for all MPRAGE scans in an MRI project in XNAT and save statistics in a spreadsheet. View Use Case.

$label.name