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USAGE
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USAGE
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ChildBrainFlow Pipeline
=======================
ChildBrainFlow is an end-to-end pipeline that performs tractography, t1 reconstruction and connectomics.
It is essentially a merged version of multiple individual pipeline to avoid the handling of inputs/outputs
between flows with some parameters tuned for pediatric brain scans. Here is a list of flows from which
process have been taken:
1. TractoFlow (https://github.com/scilus/tractoflow.git)
2. FreeSurfer-Flow (https://github.com/scilus/freesurfer_flow)
3. Connectoflow (https://github.com/scilus/connectoflow)
*** Please note that some steps have been removed from the original pipelines if they were not relevant ***
*** for pediatric data. If you need some of these steps, please use the original pipelines. ***
Steps Selection
---------------
It is possible to choose which part of the pipeline will be run by using the -profile parameter. Depending
on which -profile is selected, input files will differ. To get a list of the required input files, use this
command:
nextflow run ChildBrainFlow/main.nf --help -profile {desired_profile}
Available Profiles
------------------
Here is a list of available profiles:
1. tracking : If selected, preprocessing of DWI and Anatomical data will be performed followed by
local modelling and tractography (see [1] for details).
2. connectomics : If selected, labels registration, tractogram segmentation and connectivity will be
performed.
3. freesurfer : If selected, FreeSurfer Recon-all (or FastSurfer) will be run on input T1s and label files will be
generated (available atlases: freesurfer's atlases, Brainnetome, Brainnetome Child and Glasser).
Only available if T1 volume is supplied as input (therefore, not with -profile infant).
4. infant : If selected, the pipeline will assume the data is from infant patients (< 2 years old)
and adapt some parameters to perform tractography and connectomics.
Multiple profiles can be selected at the same time, the pipeline will simply organised channels to seemlessly
connect each steps.
To view the required input files, select all the profiles you want to run (ex: tracking, connectomics and infant)
and run this command :
nextflow run ChildBrainFlow/main.nf --help -profile tracking,connectomics,infant