QuNex HCP-Style Processing Pipeline

Document outlining the main steps for processing HCP-style data using the QuNex/HCP pipeline without a recipe.

Authors: Stephania Assimopoulos, Daniel Halls
Example dataset: HCP Development (to demonstrate path set-up)

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Overview

This repository contains shell scripts implementing a step-by-step QuNex processing workflow for HCP-style datasets. Each processing stage is executed independently once previous steps have completed successfully.

All scripts share a common configuration file (Preamble.sh) that defines environment modules and dataset-specific paths.

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Important Notes

1. Each script sources a Preamble.sh file located in the same directory as the scripts.
   Edit this file to match dataset paths and required modules.

2. Raw data must exist in the data directory specified in Preamble.sh.
   The directory structure is tied to the expected QuNex output setup. See example Preamble.sh.

3. Setup scripts are run interactively in the terminal, while processing steps can be submitted to the compute queue.

4. Each setup step should be executed independently, only after all previous steps have completed successfully.

5. The Structural processing is required for all subsequent steps.

6. Each script includes a --bind flag allowing use of symlinks by attaching original data paths inside the container environment.

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Pipeline Overview

flowchart LR

classDef stage fill:#2b2b2b,stroke:#cccccc,stroke-width:1.5px,color:#ffffff;

Setup["<div align='center'><b>Setup</b></div>
<hr/>
<div align='left'>
1. CreateStudy<br/>
2. ImportHCP<br/>
3. SetupHCP<br/>
4. CreateBatch
</div>"]

Structural["<div align='center'><b>Structural</b></div>
<hr/>
<div align='left'>
5. PreFreesurfer<br/>
6. Freesurfer<br/>
7. PostFreesurfer
</div>"]

Diffusion["<div align='center'><b>Diffusion</b></div>
<hr/>
<div align='left'>
8. DiffusionPreProc<br/>
9. BedpostX
</div>"]

Functional["<div align='center'><b>Functional</b></div>
<hr/>
<div align='left'>
10. fMRIVolume<br/>
11. fMRISurface<br/>
12. MSMALL<br/>
13. ICA
</div>"]

Setup --> Structural --> Diffusion --> Functional

class Setup,Structural,Diffusion,Functional stage;

Loading

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Pipeline Steps

1. Setup

Initial study creation and preparation.

sh ${script_repo}/CreatStudy.sh ${subject_id}
sh ${script_repo}/ImportHCP.sh ${subject_id}
sh ${script_repo}/SetupHCP.sh ${subject_id}
sh ${script_repo}/CreateBatch.sh ${subject_id}

2. Structural

Structural MR processing.

sh ${script_repo}/PreFreesurfer.sh ${subject_id} ${queue_name}
sh ${script_repo}/Freesurfer.sh ${subject_id} ${queue_name}
sh ${script_repo}/PostFreesurfer.sh ${subject_id} ${queue_name}

3. Diffusion

Diffusion processing + BedpostX

sh ${script_repo}/DiffusionPreProc.sh ${subject_id} ${queue_name}
sh ${script_repo}/BedpostX.sh ${subject_id} ${queue_name} ${model}

4. Functional

Functional preprocessing

sh ${script_repo}/fMRIVolume.sh ${subject_id} ${queue_name}
sh ${script_repo}/fMRISurface.sh ${subject_id} ${queue_name}
sh ${script_repo}/MSMALL.sh ${subject_id} ${queue_name}
sh ${script_repo}/ICA.sh ${subject_id} ${queue_name}

BONUS: fMRI QC functions

${script_repo}/quality_control.py