# chp_seg **Repository Path**: wrd666/chp_seg ## Basic Information - **Project Name**: chp_seg - **Description**: No description available - **Primary Language**: Unknown - **License**: Not specified - **Default Branch**: main - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2025-10-15 - **Last Updated**: 2025-10-15 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README # Choroid plexus segmentation ## This is a fork of https://github.com/Center-of-Imaging-Biomarker-Development/chp_seg all new updates will be released on https://github.com/Center-of-Imaging-Biomarker-Development/chp_seg Segmentation tool for the delineation and volumetric quantification of the choroid plexus ## Quick Start Instructions If you have already installed Docker, you can get the kilianhett/chp_seg:1.0.0 image from Docker Hub repository: ``` sudo docker pull kilianhett/chp_seg:1.0.0 ``` Choroid plexus segmentation software currently only supports CPU ``` sudo docker run -v /absolute_path_to_folder/:/data/in -v /absolute_path_to_folder/:/data/out kilianhett/chp_seg:1.0.0 --sequence_type T1 --name_pattern ``` See Installation instructions for detailed instructions on how to install all the dependencies. See How to use Chp_Seg for detailed instructions on how to use Chp_Seg. If you use this software please cite the [[associated publication]](https://fluidsbarrierscns.biomedcentral.com/articles/10.1186/s12987-024-00525-9) Eisma, Jarrod J., et al. "Deep learning segmentation of the choroid plexus from structural magnetic resonance imaging (MRI): validation and normative ranges across the adult lifespan." Fluids and Barriers of the CNS 21.1 (2024): 1-13. # Installation instructions ## Prerequisites To run this Docker image on a CPU, you will need: * a x86_64 CPU * At least 6GB of RAM * GNU/Linux [[supported distributions]](https://docs.docker.com/engine/install/#server), MacOS, or Windows 10/11 with WSL [[supported versions]](https://docs.docker.com/desktop/windows/install/) * Docker >= 19.03 * Chp_seg Docker image * MRI files in nifti format ## Installation Docker may be installed on supported versions of [GNU/Linux] or [Windows 10/11 with WSL]. The docker image can also be transformed in a [Singularity image] ### Docker #### Installation on MacOS Here are the detailed installation instructions on MacOS [[instructions]](https://docs.docker.com/desktop/install/mac-install/) #### Installation on GNU/Linux Here are the detailed installation instructions on Ubuntu (18.04 or above). Install Docker from the official repository [[instructions]](https://docs.docker.com/engine/install/ubuntu/). (Docker no longer releases updated packages for Ubuntu 16.04) ``` #Uninstall old versions of docker sudo apt-get remove docker docker-engine docker.io containerd runc #Install using the official repository sudo apt-get update sudo apt-get install apt-transport-https ca-certificates curl gnupg-agent software-properties-common curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - sudo apt-key fingerprint 0EBFCD88 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" sudo apt-get update sudo apt-get install docker-ce docker-ce-cli containerd.io #Verify that Docker Engine is installed correctly sudo docker run hello-world # it may download the hello-world docker image and then print "Hello from Docker!" and other information. ``` #### Installation on Windows 10/11 with WSL Here are the detailed installation instructions on Windows 10 or 11. ##### Check Windows version You need: * Windows 10 64-bit: Home or Pro 2004 (build 19041) or higher, or Enterprise or Education 1909 (build 18363) or higher. * Windows 11 64-bit: Home or Pro version 21H2 or higher, or Enterprise or Education version 21H2 or higher. To check your Windows version and build number, select Windows logo key + R, type winver, select OK. You can update to the latest Windows version by selecting Start > Settings > Windows Update > Check for updates. ##### Enable BIOS virtualization support BIOS-level hardware virtualization support must be enabled. You can check the Performance tab on the Task Manager to see if virtualization is enabled, see [virtualization support](https://docs.docker.com/desktop/windows/troubleshoot/#virtualization-must-be-enabled). ##### WSL2 Install Windows Subsystem for Linux (WSL) 2 [[instructions]](https://docs.microsoft.com/en-us/windows/wsl/install) Open PowerShell as Administrator (Start menu > PowerShell > right-click > Run as Administrator) and enter this command: ``` wsl --install ``` It should install the last Ubuntu LTS. You may need to reboot your machine. You can check that WSL version 2 was installed: Open PowerShell as Administrator (Start menu > PowerShell > right-click > Run as Administrator) and enter this command: ``` wsl -l -v ``` Launch Ubuntu (Start menu > ubuntu). It should ask to create a default user. You may upgrade the system: ``` sudo apt-get update sudo apt-get upgrade ``` # How to use ChP Segmentation ## Inputs This Docker image requires T1-weighted, T2-weighted, or FLAIR images in nifti format (.nii or .nii.gz) as inputs. To convert your DICOM files into nifti format, you can use [dcm2niix](https://github.com/rordenlab/dcm2niix), a multiplatform and open-source software. ## Outputs For each processed image, the following files will be produced and stored separately in a folder named *filename* (where *filename* is replaced by the original filename): * *filename*.nii.gz: Native image corrected for N4 inhomogeneity * *filename*_chp_mask.nii.gz: Segmentation maps of the choroid plexus structures ## Command options The Docker image has the following arguments: ``` [--sequence_type `T1/T2/FLAIR`] [--name_pattern ``] [--overwrite True/False (default=False] ``` * `T1/T2/FLAIR`: Type of sequence defined as input T1, T2, or FLAIR. * ``: Filter the filenames with a specific pattern in the input directory. * ``: Allow to replace already existing processing output.