babyAFQ_demo.zip (2.5 GB)
Code and example data
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modified on 2021-05-26, 23:24 This code is an example of how to use babyAFQ in order to identify white matter bundles in an infant whole brain connectome.
The code takes as input a wholebrain connectome, anatomy and diffusion data and identifies 26 white matter bundles. It also plots the output bundles for quality assessment. The example subject included here is a newborn; it is the same individual presented in fig 1 in the manuscript currently under consideration to enable easy comparison.
The code takes as input a wholebrain connectome, anatomy and diffusion data and identifies 26 white matter bundles. It also plots the output bundles for quality assessment. The example subject included here is a newborn; it is the same individual presented in fig 1 in the manuscript currently under consideration to enable easy comparison.
There are three folders included here. The folder "exampleSubjectOutput" shows what the babyAFQ_demo.m should generate from the files in "exampleSubjectClean". The
folder "exampleSubject" is created by the babyAFQ_demo.m and will show the files created in the current execusion of the code.
The code requires SPM (v12, https://www.fil.ion.ucl.ac.uk/spm/), VistaSoft (https://github.com/vistalab/vistasoft), as well as AFQ (https://github.com/yeatmanlab/AFQ). The code has been tested in MatlabR2015a running on Ubuntu16.
You will need to be in the "babyAFQ_demo" folder to run this code. Running the code will take several hours on an ubuntu workstation.
The code requires SPM (v12, https://www.fil.ion.ucl.ac.uk/spm/), VistaSoft (https://github.com/vistalab/vistasoft), as well as AFQ (https://github.com/yeatmanlab/AFQ). The code has been tested in MatlabR2015a running on Ubuntu16.
You will need to be in the "babyAFQ_demo" folder to run this code. Running the code will take several hours on an ubuntu workstation.
