egyptdj / hcpeppipelines

Processing pipelines for the HCP with batch script update for HCP-EP dataset

HCP-EP Pipelines

This repository contains updated example batch scripts to follow the naming convention and the imaging sequence parameters of the HCP-EP dataset. The batch scripts can be found at Examples/Scripts Currently updated scripts are

- PreFreeSurferPipelineBatch.sh
- FreeSurferPipelineBatch.sh
- PostFreeSurferPipelineBatch.sh
- GenericfMRIVolumeProcessingPipelineBatch.sh
- GenericfMRISurfaceProcessingPipelineBatch.sh
- DiffusionPreprocessingBatch.sh
- IcaFixProcessingBatch.sh
- PostFixBatch.sh
- ApplyHandReClassificationsBatch.sh
- MSMAllPipelineBatch.sh
- DeDriftAndResamplePipelineBatch.sh

Notes

• The released dataset package does not include the Native surface data. If you want to go further through fMRI surface processing and FIX denoising, you will have to run (Pre/Post)Freesurfer pipelines too.
• Scripts in this repository are based on the original HCPpipelines and is modified for personal research use. The author does not take any responsibility for any consequences of using the batch scripts from this repository.

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HCP Pipelines

The HCP Pipelines product is a set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project. Among other things, these tools implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013

For further information, please see:

• The Release Notes, Installation, and Usage document for the current release,
• The FAQ, and
• Other documentation in the project Wiki

Discussion of HCP Pipeline usage and improvements can be posted to the hcp-users discussion list. Sign up for hcp-users at http://humanconnectome.org/contact/#subscribe