README.txt 2.22 KB
Newer Older
Matteo Bastiani's avatar
Matteo Bastiani committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
dHCP neonatal dMRI data processing pipeline
March, 2018

V 0.0.1: Pipeline reflecting the first data release processing
Comprehensive and automated pipeline to consistently analyse neonatal dMRI data from the developing Human Connectome Project (dHCP).

If you use the pipeline in your work, please cite the following article:
Bastiani, M., Andersson, J., Cordero-Grande, L., Murgasova, M., Hutter, J., Price, A.N., Makropoulos, A., Fitzgibbon, S.P., Hughes, E., Rueckert, D., Victor, S., Rutherford, M., Edwards, A.D., Smith, S., Tournier, J.-D., Hajnal, J.V., Jbabdi, S., Sotiropoulos, S.N. (2018). Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project. NeuroImage. 

The pipeline consists of several bash scripts.
Once it has been downloaded, the first thing to do is fill the correct paths into:

The script needs to be run before launching the processing jobs.

To launch the pipeline for a single subject, use the following command:
${scriptsFolder}/ ${rawDataFolder}/sub-${cid} ses-${no} ${rawDataFile} ${cid} ${scriptsFolder}/dhcp300_f.txt ${outFolder} ${age} ${birth} ${n_sessions}

This command will submit all the necessary scripts to process the raw dMRI data. The necessary inputs are:
${rawDataFolder}/sub-${cid}: Path to raw data
ses-${no}: Session number
${rawDataFile}: Raw data file name
${cid}: Connectome ID
${scriptsFolder}/dhcp300_f.txt: Protocol file
${outFolder}: Output folder
${age}: Age at scan (in rounded weeks)
${birth}: Age at birth (in rounded weeks)
${n_sessions}: Total number of scanning sessions for the same subject

Non-dHCP data
To convert a locally acquired dataset such that it can be used with the pipeline, use the command:

By typing the command in a terminal, the necessary inputs will be shown.
The script will generate a raw data file and a protocol file that can be used with the pipeline.