BrainWavelet Toolbox

This toolbox contains the Wavelet Despiking algorithm described in:

Patel AX et al. A wavelet method for modeling and despiking motion artifacts from resting-state fMRI time series. NeuroImage (2014). 95:287-304. [http://dx.doi.org/10.1016/j.neuroimage.2014.03.012.]


VERSION 2.0 as described in

Patel AX and Bullmore ET (2015) A wavelet-based estimator of the degrees of freedom in denoised fMRI time series for probabilistic testing of functional connectivity and brain graphs. NeuroImage. in press.   (http://dx.doi.org/10.1016/j.neuroimage.2015.04.052)

is COMING SOON!! EXPECTED RELEASE DATE: July 1st 2015.


The toolbox is written in MATLAB, and was designed to be used as an add-on module to existing data pre-processing pipelines. There are two editions available: the ‘fMRI Edition’ and the ‘matrix edition’. The ‘fMRI edition’ (recommended for Neuroimagers) takes NIfTI file inputs and will output despiked NIfTI files. This edition also includes a number of additional features, including Spike Percentage calculation, as described in the above paper. The ‘Matrix Edition’ implements the same algorithm on a 2D matrix of time series, and was designed for use with other biological time series.

There are releases for different operating systems, indicated by the download labels below. If you are running Mac OS X Snow Leopard, Lion or Mountain Lion, please download the Snow Leopard+ release. Guidelines on installation and setup are provided in the ‘Documentation’ subfolder of the download.

A comprehensive list of updates can be viewed in the change log.

fMRI Edition v1.0 beta
07-Feb-2014 ** Launch **

Matrix Edition v1.0 beta
10-Feb-2014 ** Launch **

fMRI Edition v1.1
10-Feb-2014 ** Launch **
10-Feb-2014 ** v1.0 Bug Fix ** Spike Percentage calculation with Batch Mode.
10-Feb-2014 ** v1.0 Bug Fix ** Release for OSX Mavericks to prevent MemorySolver crash.
10-Feb-2014 ** Added option ** Allow oblique NIfTI input.
27-Mar-2014 ** v1.1 Bug Fix ** Fixed oblique NIfTI input crash.

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Please select the appropriate toolbox version from the check-box list below, and fill out your details on the form that appears to receive your download. This is in order for you to receive high priority updates and bug fixes via email as soon as they become available. After submitting your details and accepting the terms and conditions of use outlined in the license agreement, a download link will appear. Thank you for downloading!

Brain Wavelet Toolbox

Copyright © Ameera X Patel (2013, 2014), University of Cambridge

All rights reserved.

Please cite the following article if you use any of this code in a publication:

Patel AX, Kundu P, Rubinov M, Jones PS, Vertes PE, Ersche KD, Suckling J, Bullmore ET. A wavelet method for modeling and despiking motion artifacts from resting-state fMRI time series. NeuroImage (2014). 95:287-304. [http://dx.doi.org/10.1016/j.neuroimage.2014.03.012.].

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Redistribution of any code or files in this toolbox (in any form, electronic or mechanical) and use in source and binary forms, with or without modification, are not permitted without the express permission of the author.

Neither the name of the owner nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

You are not permitted under this License to use this software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the software to provide any service to an external organisation for which payment is received.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

You may be held legally responsible for any copyright infringement that is caused or encouraged by your failure to abide by these terms and conditions.

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BWT v1.1 -- fMRI Edition -- OSX Mavericks
BWT v1.1 -- fMRI Edition -- OSX SnowLeopard+
BWT v1.1 -- fMRI Edition -- Linux/Windows
BWT v1.0 -- Matrix Edition -- OSX Mavericks
BWT v1.0 -- Matrix Edition -- OSX SnowLeopard+
BWT v1.0 -- Matrix Edition -- Linux/Windows

 

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