[RESOLVED] Customizing mapping.txt and batch.txt files

[grw201]

I’m a neuroscience PhD student using HCP’s minimal preprocessing pipelines for my dissertation research. I installed QuNex and downloaded the exemplar mapping.txt and batch.txt files but can’t find any documentation on how to edit them to accommodate my data. I’m using locally collected data which has different scan parameters and is lacking T2 images which means I need to make significant edits to the aforementioned files and use the LegacyStyleData argument. However, as stated I can’t figure out exactly how to do this or where to make these edits. Is there any documentation I’m missing that explains this?

Thank you,

Graham

[demsarjure]

Hi Graham,

Welcome to the QuNex forums!

QuNex documentation is a good way to start, I would recommend going over the following pages:

• QuickStart - onboards DICOM data and prepares everything that is required for HCP processing (
  QuNex quick start using a Docker container — QuNex documentation). In there you will find examples of all the necessary files for data acquired with the HCP imaging protocol. I would suggest you to use route B, which does things step-by-step. You can use the downloaded mapping and parameter/batch files as templates for your files.

• Documentation on mapping files: Preparing a study-level mapping file for QuNex workflows — QuNex documentation.

• Documentation on batch files: Batch files — QuNex documentation.

You can also post the full command chain that you executed here, along with created files and we can help you out with preparation of command calls and support files for steps that follow.

Jure

[demsarjure]

Graham, did you manage to resolve the issues that you mentioning in the original post? If not, please let us know where you are stuck and we will help out.