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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-02-05T07:32:57.335Z","updated_at":"2026-02-05T07:32:57.981Z","avatar_url":"https://github.com/khanlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Structural Connectivity Applied To Targeted Regions (SCATTR)\n[![Documentation Status](https://readthedocs.org/projects/scattr/badge/?version=stable)](https://scattr.readthedocs.io/en/stable/?badge=stable)\n![Version](https://img.shields.io/github/v/tag/khanlab/scattr?label=version)\n![Python3](https://img.shields.io/badge/python-3.8_|_3.9_|_3.10_|_3.11-blue.svg)\n[![Tests](https://github.com/khanlab/scattr/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/khanlab/scattr/actions/workflows/test.yml?query=branch%3Amain)\n![Docker Pulls](https://img.shields.io/docker/pulls/khanlab/scattr)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7636506.svg)](https://doi.org/10.5281/zenodo.7636506)\n\nSCATTR is a BIDS App that performs a tractography processing workflow to \nidentify connections between targetted structures of interest (extracted from\nvarious atlases) in the brain, using some common neuroimaging tools like \n`prepdwi`, `Freesurfer`, and `Mrtrix3`.\n\n![Example outputs](https://raw.githubusercontent.com/khanlab/scattr/main/docs/images/ex_output.png)\n\nThis is useful for:\n\n* Analyzing structural connections of known brain circuits\n* Examining specific connections of interest\n* Comparison across different groups (e.g. controls vs patients)\n\n\n## Example use of workflow \nThis workflow was used to process and analyze the data from\n[`hcp_subcortical_repo`](https://github.com/kaitj/hcp_subcortical_repro) \n(see Kai et al., 2022). \n\n## Workflow \nA brief summary of the workflow can be found below (see documentation for\na detailed summary):\n\n_Note: The workflow assumes Freesurfer has already been run on the dataset, as \nwell as diffusion preprocessing (e.g. distortion correction)._\n\n![Workflow example](https://raw.githubusercontent.com/khanlab/scattr/main/docs/images/workflow.png)\n\n1. Merge the segmentations of structures in a standard template space from \nvarious sources (if necessary) via \n[labelmerge](https://zenodo.org/record/7636410) into a combined atlas, which is \nused downstream to identify targeted connections.\n1. Estimate and apply transformations from standard template space to \nsubject-specific space.\n1. Further process the pre-processed diffusion data to enable tractography\n(e.g. compute response functions, fibre orientation distribution, \nnormalization).\n1. Perform whole-brain tractography from computed files, applying filtering \n(e.g. SIFT2) to computed tractogram. Once filtered, connections between the \nmerged segmentations (from step 1) are identified, generating a connectome map.\n1. Analysis can then be performed on the map to examine and explore the \nconnectome of interest.\n\n### **Full documentation:** [here](https://scattr.readthedocs.io/en/stable/)\n\n## Relevant Papers\n\n* Kai, J., Khan, A.R., Haast, R.A.M., Lau, J.C. (2022).\nMapping the subcortical connectome using in vivo diffusion MRI: feasibility\nand reliability. Terra incognita: diving into the human subcortex,\nspecial issue of NeuroImage. doi: \n[10.1016/j.neuroimage.2022.119553](https://doi.org/10.1016/j.neuroimage.2022.119553).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkhanlab%2Fscattr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkhanlab%2Fscattr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkhanlab%2Fscattr/lists"}