masidocker/harmonizeapp repository overview

Each pipeline has its own BIDS App named from the tag.

Currently, we have these pipelines ready for BIDS App:

T1

• SLANT-TICV v1.2 (masidocker/harmonizeapp:slant-ticv)
• MaCRUISE v 3.2.0 (masidocker/harmonizeapp:macruise)
• BISCUIT v2.2 (masidocker/harmonizeapp:biscuit)
• FreeSurfer 7.4.1 (masidocker/harmonizeapp:freesurfer7)

Diffusion

• PreQual (masidocker/harmonizeapp:prequal)
• Atlas Registration (EVE3 and MNI) (masidocker/harmonizeapp:atlasreg)
• Connectome Special (masidocker/harmonizeapp:connectome-special)
• Francois Special (masidocker/harmonizeapp:francoisSpecial)
• TractSeg (masidocker/harmonizeapp:tractseg)
• FreeWater (masidocker/harmonizeapp:freewater)

⁠==== HOW TO RUN

To pull a BIDS App docker,

docker pull masidocker/harmonizeapp:<appname>

To run specific app, make sure your data is in BIDS format.

docker run --privileged -v <path_to_bids_directory>:/bids_dir -v <path_to_output_directory>:/output_dir <docker_name> /bids_dir /output_dir participant --haveses <0|1> [options]

Options:

[REQUIRED] --haveses [0|1]       : indicate whether the dataset has a session or not (0 for no, 1 for yes)
[OPTIONAL] --subject [sub-name]  : the subject (and session) to be run. Default: all subjects. 
                                   Example: --subject sub-BLSA0000
                                            --subject sub-BLSA0000/ses-020scanner10
[OPTIONAL] --acq [acq_name]      : the acquisition of the subject(s) listed in `--subject`. 
[OPTIONAL] --run [run_name]      : the run number of the subject(s) listed in `--subject`.
[REQUIRED] --EVE3                : [Only for Atlas Registration] For White Matter EVE3 Atlas Diffusion Registration
[REQUIRED] --MNI                 : [Only for Atlas Registration] For MNI Atlas Diffusion Registration 

Examples:

docker run --privileged -v /nfs/BIDS/DATASET/:/bids_dir -v /nfs/BIDS/DATASET/derivatives/:/output_dir masidocker/harmonizeapp:MaCRUISEv3.2.0 /bids_dir /output_dir participant --haveses 1

docker run --privileged -v /nfs/BIDS/DATASET/:/bids_dir -v /nfs/BIDS/DATASET/derivatives/:/output_dir masidocker/harmonizeapp:SLANT-TICVv1.2 /bids_dir /output_dir participant --haveses 0 --subject sub-001 sub-002 --acq MPRAGE --run 1

docker run --privileged -v /nfs/BIDS/DATASET/:/bids_dir -v /nfs/BIDS/DATASET/derivatives/:/output_dir masidocker/harmonizeapp:AtlasReg /bids_dir /output_dir participant --haveses 1 --run 1 --EVE3

For any questions, contact [email protected]⁠ / [email protected]⁠