RISE/NeuroHUB

Requirements: Docker Desktop, Filezilla

Downloading these tools is simple. Navigate to the website and download.

Docker: https://www.docker.com/products/docker-desktop/

Filezilla: https://filezilla-project.org/

Download data from CBIHome

Open Filezilla

Host: sftp://cbihome.musc.edu
Username: [your netID]
Password: [your netID password]

Set download location to RISE/NeuroHUB Imaging folder

Naviagate to /MRData/Aghamoosa/[Study]

Download new scans

Double click the new scans. They will be downloaded to the [study]_imaging folder.

Organize Raw Data

Open a Terminal/Power Shell window

Mac: Open Applications folder -> Utilities -> Terminal.app

Windows: Open Start -> type "PowerShell" -> open PowerShell

If you are running the script for the first time, pull the Docker image

docker pull regularsizedryn/rise-nh-bids:1.0

Enter the following command for NeuroHub

Mac:

docker run --rm
-v /Volumes/vdrive/helpern_users/aghamoosa_s/NeuroHUB/NeuroHUB_Imaging:/input
-v /Volumes/vdrive/helpern_users/aghamoosa_s/NeuroHUB/NeuroHUB_Imaging/BIDS:/output
rise-nh-bids
--input /input
--output /output
--overwrite

Windows:

docker run --rm -v "/Volumes/vdrive/helpern_users/aghamoosa_s/NeuroHUB/NeuroHUB_Imaging:/input" -v "/Volumes/vdrive/helpern_users/aghamoosa_s/NeuroHUB/NeuroHUB_Imaging/BIDS:/output" regularsizedryn/rise-nh-bids:1.0 --input /input --output /output --overwrite

Or the following command for RISE

docker run --rm
-v /Volumes/vdrive/helpern_users/aghamoosa_s/RISE/RISE_Imaging:/input
-v /Volumes/vdrive/helpern_users/aghamoosa_s/RISE/RISE_Imaging/BIDS:/output
rise-nh-bids
--input /input
--output /output
--overwrite

Windows:

docker run --rm -v "/Volumes/vdrive/helpern_users/aghamoosa_s/RISE/RISE_Imaging:/input" -v "/Volumes/vdrive/helpern_users/aghamoosa_s/RISE/RISE_Imaging/BIDS:/output" regularsizedryn/rise-nh-bids:1.0 --input /input --output /output --overwrite

QC Data

See QC guides here.