NIH Blueprint: The Human Connectome Project

HCP Pipelines Reference

Release date: Sep 10, 2014.

IMPORTANT: Before you begin to use HCP Data, please review the set of available HCP Data Use Terms, and follow the steps to accept the terms that apply to your research.

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.

Download HCP Pipelines from Github

Release notes

  1. The HCP Pipelines scripts are being released in essentially the form that they were successfully used for processing data provided in the Human Connectome Project 500 Subjects Data Release. That processing was done using 64-bit Red Hat Linux version 5.

  2. Some improvements to the documentation have been made since they were used for that release.

  3. One known difference between these scripts as they were used for the 500 Subjects Data Release and their currently released form is the version of the wb_command from the Connectome Workbench that is used.

    When these scripts were being used for the 500 Subjects Data Release, Connectome Workbench had not reached its 1.0 release level. Therefore, we used an earlier version of the wb_command for processing data for the data release. Distributing that older version of the wb_command binary as part of this product is less than ideal because that embedded binary is platform specific and is not part of an official Connectome Workbench release.

    If needed, the Red Hat/CentOS specific version of the wb_command binary and it associated libraries used are available in older, tagged, pre-release versions of this project.

  4. We have begun the process of making the scripts more robust, well-documented, and usable in other environments (other versions of operating systems, other queueing systems, other versions of prerequisite tools, etc.) But that process is not complete. Therefore, we cannot guarantee that you will not have to make modifications to the scripts for them to be used successfully in your environment.

  5. A significant part of the value of the open source model of software development is the ability to improve software based on source code level feedback from the community of users. Along those lines, if you find that you do need to make changes to the source code to use the tools successfully, we would welcome feedback and improvement suggestions. (If you have to change something in the scripts to make them work for you, let us know and we'll evaluate how/if to incorporate those changes into the released product.)

    Discussion of HCP Pipeline usage and improvements can be posted to the hcp-users discussion list. Sign up for hcp-users at

  6. For the HCP 500 Subjects Data Release, FSL version 5.0.6 was used with these scripts. There is a known issue with using FSL 5.0.7 for the Task fMRI Analysis Pipeline.

  7. Improvements to the internal documentation of these scripts are planned.

  8. Validation tests to ensure that your installation is working correctly with at least the sample data are also planned but not yet available.

Full Release Notes

Frequently Asked Questions

Answers to frequently asked questions can be found on our Github Repository: HCP Pipeline FAQ.