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.
Useful for:
- developing or running image processing locally in bash shell;using
- usin XNAT as data source and/or remote archive in shell scripts;
- automating processing of multiple XNAT sessions and to reporting results in spreadsheets.
- focusing on local script development and minimizing programming effort to interact with XNAT.
Installing XTOLM
Client machine prerequisites to run XTOLM on a 64 bit Linux:
- Download xtolm
- Download XNAT tools and Java 1.8 if you plan to upload data back to XNAT
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 |
Built-in varaiables (online mode only)
| xt_server | https://my_xnat_server |
|---|---|
| xt_user | xnat_user |
| xt_pass | xnat_password |
| xt_project | xnat_project |
| xt_subj | xnat_subject |
| xt_sess | xnat_experiment |
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:
Other commands
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.
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.