GitHub - yeatmanlab/AFQ: Automated Fiber Quantification

8 Branches 3 Tags

Name	Name	Last commit message	Last commit date
Latest commit jyeatman Merge pull request #47 from yeatmanlab/cp-prob-seg Oct 10, 2023 2df10b9 · Oct 10, 2023 History 638 Commits
3Dmesh	3Dmesh	added new example for coloring fiber nodes	Dec 9, 2020
SIPS	SIPS	Add SIPS folder	Aug 31, 2017
SLF123	SLF123	added SLF123 from Romi Sagi1, J.S.H. Taylor, Kyriaki Neophytou, Tamar…	Aug 22, 2023
aslant	aslant	new functions	Mar 23, 2018
babyAFQ	babyAFQ	Added link to demo to readme file	Mar 30, 2021
cerebellarPeduncles	cerebellarPeduncles	code from Bruckert et al to segment cerebellar peduncles	Jan 31, 2019
cp-prob_segmentation	cp-prob_segmentation	new cp probabilistic segmentation	Oct 10, 2023
data	data	added more example data	Mar 13, 2013
functions	functions	Added comments to each function to explain difference between bbAFQ a…	Sep 8, 2020
gui	gui	minor changes	Sep 12, 2014
templates	templates	Merge branch 'master' of https://github.com/jyeatman/afq	Aug 12, 2015
test	test	added more tests	Nov 19, 2012
tutorials	tutorials	updated video write code	Oct 23, 2018
utilities	utilities	Added comments to each function to explain difference between bbAFQ a…	Sep 8, 2020
vof	vof	moving to the server	Jul 8, 2016
.gitignore	.gitignore	organizing directories	Nov 18, 2012
AFQ_Poster_SfN_2012.pdf	AFQ_Poster_SfN_2012.pdf	Added options to change the relative weighting of each fiber when com…	Nov 6, 2012
README.txt	README.txt	Update README.txt	Oct 23, 2021
TODO.txt	TODO.txt	to do list	Nov 26, 2012
Yeatman_PLoSONE_2012.pdf	Yeatman_PLoSONE_2012.pdf	Added the published AFQ manuscript	Nov 22, 2012

Repository files navigation

AFQ version 1.2

==============================
Automated Fiber Quantification
==============================

AFQ was designed to generate Tract Profiles of tissue properties for major fiber tracts in healthy and diseased brains. Online documentation can be found at: 
https://github.com/yeatmanlab/AFQ/wiki.
We have now released pyAFQ and all current development is occuring on the Python version: https://github.com/yeatmanlab/pyAFQ
For help and updates on MATLAB join the AFQ mailing list in google groups:
https://groups.google.com/forum/?fromgroups#!forum/automated-fiber-quantification-afq

AFQ has been tested for MATLAB r2009b through MATLAB r2021. It requires functions from the MATLAB stats toolbox, vistasoft and SPM.

If you use this software please cite the relevant manuscripts describing the work:

(v0.1)  —  Yeatman J.D., Dougherty R.F., Myall N.J., Wandell B.A., Feldman H.M. (2012). Tract Profiles of White Matter Properties: Automating Fiber-Tract Quantification. PLoS One.

(v1.1)  —  Yeatman J.D., Wandell B.A., Mezer A. (2014). Lifespan Maturation and Degeneration of Human Brain White Matter. Nature Communications.

(v1.2)  —  Yeatman J.D., Weiner K.S., Pestilli F., Rokem A., Mezer A., Wandell B.A. (2014). The Vertical Occipital Fasciculus: A Century of Controversy Resolved By In Vivo Measurements. PNAS.

pyAFQ is described in:
Kruper J., Yeatman J.D., Richie-Halford A., Bloom D., Grotheer M., Caffarra S., Kiar G., Karipidis I.I., Roy, E., Chandio B.Q., Garyfallidis E., Rokem A. (2021). Evaluating the reliability of human brain white matter tractometry. Aperture
https://www.humanbrainmapping.org/files/Aperture/Accepted%20Works%20PDF/Kruper_Evaluating_the_Reliability_of_Human.pdf

    Copyright (C) 2012   Jason D. Yeatman   [email protected]

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details http://www.gnu.org/licenses/