Job Jar/DTI pipeline GUI

The Diffusion Processing Pipeline is a series of command-line programs that our group uses to convert brain scan data into an intermediate representation called a "diffusion tensor image" (or DTI) and lastly into a so-called "streamtube" model, where apparent structures in the brain are represented by narrow, curving tubes in space.

We receive data from many different collaborators around the world, and each person uses slightly different scanning parameters and represents their output in a different data format. Therefore, while running a given dataset through the pipeline is almost exactly the same as running any other one through, there are always subtle differences.

Other research groups have similar suites of non-interactive command-line tools, but also have graphical user interface (GUI) wrapper programs for running each individual step or even the whole pipeline. Two examples are FSL, from the University of Oxford, and DTK from Massachusetts General Hospital. Both of these programs are installed on the Linux systems in the department; simply type fsl or dtk at the command line to look at either one.

We'd like to create a similar piece of software to run our pipeline. In particular, the GUI program should include all the common options for each of the five major steps of the processing pipeline, plus common presets, and its output should be a sequence of calls to the pipeline programs. The user should be able to preview this sequence of calls, run it, and also export it to a Makefile that can then be re-used for other datasets. As such it is imperative that the automatically generated program calls use relative paths rather than absolute paths.

Jadrian has been running and developing the bulk of the pipeline for the last couple years and would be the main contact person for this job.

This is a screenshot of the DTK GUI, which can provide some inspiration for what our GUI might look like (click for a full-size image):