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BrettNordin/fMRIprep.dcm2niix

fMRIprep.dcm2niix is designed to convert DICOM format to the NIfTI format.

Installation

The repository has been desgined to run either in Docker or Singularity:

Docker Link

Singularity Link

Docker Usage

docker run --rm -it -v /Volumes/DriveA/InputData:/input -v /Volumes/DriveA/OutputData:/output brettnordin/fmriprep.dcm2nii:latest -i /input -o /output

Please replace "/Volumes/DriveA/InputData" and "/Volumes/DriveA/OutputData" with the correct directory locations for your project.

Additonal options:

-p "sub-1 sub-2"    Specify specific participants to run, seperated by a space and encapsuated by quotation marks. Excluding this option will run all participants located in the input folder.

-c Y    Specifying "-c Y" enables root decompression. Only enable this if the root subject folder in the input files in compressed (.tgz only)

Singularity Usage

singularity run --cleanenv -B /Volumes/DriveA/InputData:/input -B /Volumes/DriveA/OutputData:/output library://brettnordin/default/dcm2niix -i /input -o /output 

Please replace "/Volumes/DriveA/InputData" and "/Volumes/DriveA/OutputData" with the correct directory locations for your project.

Additonal options:

 -p "sub-1 sub-2"    Specify specific participants to run, seperated by a space and encapsuated by quotation marks. Excluding this option will run all participants located in the input folder.
 
-c Y    Specifying "-c Y" enables root decompression. Only enable this if the root subject folder in the input files in compressed (.tgz only)

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Whats included:

Base image: ubuntu:bionic-20201119

Apt-Package jo: jo Github

Apt-Package jq: jq Github

Apt-Package pigz: pigz Github

Apt-Package dcm2niix: dcm2niix Github