🧠 LOBI Scripts for MRI Data Processing

This repository contains custom dcm2bids configuration files for our projects and run scripts for common MRI processing tasks such as MRIQC, fMRIPrep, and FreeSurfer setup.

For guidance on using the Neurodesk platform, see quickstart.md and FAQ.md. The quickstart tutorial shows how to use Neurodesk, the xnat_dcm2bids module, and the scripts provided in this repository, while the FAQ covers practical platform-related questions.

Specifically, this repository provides the following resources:

📁 dcm2bids configs

Custom configuration files for our projects: ➡️ ./dcm2bids

⚙️ Available run scripts

• run_mriqc.sh subject bids_dir Runs MRIQC with custom resource settings and working directory. The framewise displacement (FD) threshold is set to 0.3 (adjust if needed).

• run_fmriprep_min.sh subject bids_dir Runs fMRIPrep with custom resource settings and working directory, without FreeSurfer reconstruction.

• run_fmriprep_kids_alicja.sh subject bids_dir Fully customized fMRIPrep pipeline with:

  • cohort-specific atlas from TemplateFlow,
  • BIDS filtering to include only specific task names and selected fieldmaps without the run-xx label (note: fMRIPrep will not report missing fieldmaps but gives an error when there are multiple ones available).

• freesurfer/freesurfer_init.sh subjects_dir Initializes environment variables and Freeview aliases.

• run_dcm2bids_noauto.sh xnat_id subject [session] ⚠️ Deprecated: this script has been replaced by the xnat_dcm2bids module with the flag --auto_extract_entities False.
  Caution: currently, fMRIPrep does not recognize BIDS-URIs produced by dcm2bids and the run_dcm2bids_noauto.sh script. Please repair fieldmap JSONs using the following command: find bids_root -iname "*dir*.json" -exec ./fmriprep/json_fmaps_repair.sh {} \;

We recommend working with copies of the scripts in your projects.

Typical workflow:

1. Update repository using git pull or lobi_scripts update (see below)
2. Copy a script into your project ./bids-dir/code directory.
3. Edit the local copy.
4. Run the script from your project directory.

When using the xnat_dcm2bids module, you can use the lobi_scripts shortcuts:

lobi_scripts install
lobi_scripts update

lobi_scripts ls
lobi_scripts add run_mriqc.sh ~/bids-dir/code

~/bids-dir/code/run_mriqc.sh 03 ~/bids-dir ~/bids-dir/derivatives/mriqc