Biomarker based on functional connectivity (FcBm)

Detail

Language

English

Title

Free Keywords

Description

Date

Mar 3, 2016

Last Modified Date

Dec 9, 2016 16:37:57

Created Date

Mar 3, 2016 19:01:02

Contributor

Giuseppe Lisi (glisi)

Item Type

Tool

Change Log(History)

Dec 9, 2016	Modified; Readme, Rights, Tool file.
Mar 4, 2016	Modified; Index.
Mar 4, 2016	Modified; Index.
Mar 3, 2016	Modified; Index.

Tool type

Matlab

Developer

Giuseppe Lisi

Jun Morimoto

Noriaki Yahata

Preview

Tool file

FcBm_NatComm_v1.2.zip 22077626 bytes (Login User only)

Readme

Biomarker based on functional connectivity (FcBm)

Version Hystory:
v1.1 - Original upload
v1.2 - L1-SCCA is implemented in Matlab

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Instructions to visualize the main results of the paper:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1. download and install SLR from http://www.cns.atr.jp/~oyamashi/SLR_WEB.html, and assign the corresponding path to the variable SLRdir in bm_defpar.m 
2. execute bm_eval.m to evaluate the results

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Instructions to execute the code and reproduce the results of the paper
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1. download and install SLR from http://www.cns.atr.jp/~oyamashi/SLR_WEB.html, and assign the corresponding path to the variable SLRdir in bm_defpar.m 
2. execute bm_run_no_cluster.m to compute the models on the Japanese dataset
3. execute bm_loso_std_ext.m to compute the models for the US dataset
4. execute bm_eval.m to evaluate the results

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Additional notes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1. If the files FcBm_NatComm/output/nested/[1-9]/cca_res.mat exist, L1-SCCA is not recomputed
2. If you have a computer cluster you can substitite bm_run_no_cluster.m with your own cluster command. This makes the computation much faster.
3. If you use a computer cluster, make sure that the number of nodes correspond to the variable outer_k_folds in bm_defpar.m
4. In folder FcBm_NatComm/data/, the files _COR.mat contain the Functional Connectivities and the files _SUB.dat contain the diagnostic label and demographic information (only numbers).
5. If you want to use this code with your own data, you have to customize the file bm_defpar.m


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Referencing the code
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When using this tool for a paper please refer to the following paper: 

Noriaki Yahata, Jun Morimoto, Ryuichiro Hashimoto, Giuseppe Lisi, Kazuhisa Shibata, Yuki Kawakubo, Hitoshi Kuwabara,Miho Kuroda, Takashi Yamada, Fukuda Megumi, Hiroshi Imamizu, Jose E. Nanez, Hidehiko Takahashi, Yasumasa Okamoto, Kiyoto Kasai, Nobumasa Kato, Yuka Sasaki, Takeo Watanabe, and Mitsuo Kawato (2016).
A Small Number of Abnormal Brain Connections Predicts Adult Autism Spectrum Disorder, NatComms

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Feedback & Bug report  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Any feedback and bug report are welcome. Please contact Giuseppe Lisi (glisi@atr.jp).

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Licencing & Copy Right
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Copyright (c) 2016, Advanced Telecommunications Research Institute International (ATR)
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
* Neither the name of the ATR nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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 ATR 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.

FcBm – Biomarker based on functional connectivity, Release 2016, Advanced Telecommunications Research Institute International (ATR), Kyoto, Japan (the "Software").
The Software remains the property of the ATR, and the ATR reserves the Intellectual Property (IP) rights of the Software. The Software is distributed "AS IS" through a secure server with the prior consent of the server administrator, and provided free solely for non-commercial use by a not-for-profit entity (e.g. a non-profit educational organization) in the hope that it will be useful, but in order that the ATR protects its assets.
Please note that any for-profit entity desiring to manufacture, use or sell the Software (including the modified Software) must give notice to the ATR in order to obtain a license from it (patent@atr.jp).

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Acknowledgements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This toolbox is brought to you by ATR Computational Neuroscience laboratories in Kyoto.

Rights

Copyright (c) 2016, Advanced Telecommunications Research Institute International (ATR)
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
* Neither the name of the ATR nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

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 ATR 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.

FcBm – Biomarker based on functional connectivity, Release 2016, Advanced Telecommunications Research Institute International (ATR), Kyoto, Japan (the "Software").
The Software remains the property of the ATR, and the ATR reserves the Intellectual Property (IP) rights of the Software. The Software is distributed "AS IS" through a secure server with the prior consent of the server administrator, and provided free solely for non-commercial use by a not-for-profit entity (e.g. a non-profit educational organization) in the hope that it will be useful, but in order that the ATR protects its assets.
Please note that any for-profit entity desiring to manufacture, use or sell the Software (including the modified Software) must give notice to the ATR in order to obtain a license from it (patent@atr.jp).

Index

/ Public / FcBm

Related to