Preparing study-level batch file and parameters for QuNex workflows#

Gathering relevant parameters across image modalities#

To run HCP preprocessing, especially when making use of all of the supported features (e.g. distortion correction), information on image sequences needs to be collected to be then passed to HCP preprocessing commands either as in-line parameters or listed in a batch file. This information can be found in scanner settings or stored study cards, but it is often more convenient to retrieve the information from the DICOM files directly. Do note that DICOM files can differ between MR scanner brands, models and software versions. The same information can be stored under different names and fields, or using different units, so do double check that you are extracting the correct information.

A number of tools are available for inspection of DICOM files. One option is to use AFNI dicom_hdr.

See also this thread on FSL boards for specific information on how to get the dwell time information.

The specific information you will need to be able to perform each of the steps will be listed with each step description below.

Compiling a group batch file and adding session-specific information#

Once all the data is gathered, it needs to be compiled into a single group batch file. These files (commonly named batch.txt) list information for all the sessions, as well as study parameters, so that they do not have to be specified with each invocation of the preprocessing commands. The key advantage here is that for rapid re-processing or specification of new parameters, even within a single study, use of batch files accelerates this workflow. For the specific information on batch file format, please see the batch documentation page wiki page.

To help with compilation of batch files, QuNex provides a convenience command:

  • create_batch. The command scours all the subfolders in the study sessions directory for the specified session information files and joins them in the specified target file. If desired, the sessions to add can be specified explicitly or taken from another batch or list file. Visit command's online reference or run qunex ?create_batch for more detailed information on the command usage.