Mask_explorer: A tool for exploring brain masks in fMRI group
analysis

J 2016

Mask_explorer: A tool for exploring brain masks in fMRI group analysis

GAJDOŠ, Martin; Michal MIKL a Radek MAREČEK

Základní údaje

Originální název

Mask_explorer: A tool for exploring brain masks in fMRI group analysis

Autoři

GAJDOŠ, Martin ; Michal MIKL a Radek MAREČEK

Vydání

Computer Methods and Programs in Biomedicine, Clare, Elsevier Ireland LTD, 2016, 0169-2607

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30000 3. Medical and Health Sciences

Stát vydavatele

Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.503

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/16:00088146

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1016/j.cmpb.2016.07.015

UT WoS

000381647000014

EID Scopus

2-s2.0-84978370348

Klíčová slova anglicky

fMRI; Group analysis; Dataset explorer; Preprocessing; Statistical parametric mapping; Tool

Štítky

rivok

Změněno: 15. 9. 2016 15:57, Mgr. Eva Špillingová

Anotace

V originále

Background and objective: Functional magnetic resonance imaging (fMRI) studies of the human brain are appearing in increasing numbers, providing interesting information about this complex system. Unique information about healthy and diseased brains is inferred using many types of experiments and analyses. In order to obtain reliable information, it is necessary to conduct consistent experiments with large samples of subjects and to involve statistical methods to confirm or reject any tested hypotheses. Group analysis is performed for all voxels within a group mask, i.e. a common space where all of the involved subjects contribute information. To our knowledge, a user-friendly interface with the ability to visualize subject-specific details in a common analysis space did not yet exist. The purpose of our work is to develop and present such interface. Methods: Several pitfalls have to be avoided while preparing fMRI data for group analysis. One such pitfall is spurious non-detection, caused by inferring conclusions in the volume of a group mask that has been corrupted due to a preprocessing failure. We describe a MATLAB toolbox, called the mask_explorer, designed for prevention of this pitfall. Results: The mask_explorer uses a graphical user interface, enables a user-friendly exploration of subject masks and is freely available. It is able to compute subject masks from raw data and create lists of subjects with potentially problematic data. It runs under MATLAB with the widely used SPM toolbox. Moreover, we present several practical examples where the mask_explorer is usefully applied. Conclusions: The mask_explorer is designed to quickly control the quality of the group fMRI analysis volume and to identify specific failures related to preprocessing steps and acquisition. It helps researchers detect subjects with potentially problematic data and consequently enables inspection of the data. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

GA14-33143S, projekt VaV

Název: Vliv fyziologických procesů na reliabilitu a časovou proměnlivost konektivity v lidském mozku měřené pomocí fMRI

Investor: Grantová agentura ČR, Vliv fyziologických procesů na reliabilitu a časovou proměnlivost konektivity v lidském mozku měřené pomocí fMRI

Citovat

GAJDOŠ, Martin; Michal MIKL a Radek MAREČEK. Mask_explorer: A tool for exploring brain masks in fMRI group analysis. Computer Methods and Programs in Biomedicine. Clare: Elsevier Ireland LTD, 2016, roč. 134, October, s. 155-163. ISSN 0169-2607. Dostupné z: https://doi.org/10.1016/j.cmpb.2016.07.015.

@article{1354130,
   author = {Gajdoš, Martin and Mikl, Michal and Mareček, Radek},
   article_location = {Clare},
   article_number = {October},
   doi = {https://doi.org/10.1016/j.cmpb.2016.07.015},
   keywords = {fMRI; Group analysis; Dataset explorer; Preprocessing; Statistical parametric mapping; Tool},
   language = {eng},
   issn = {0169-2607},
   journal = {Computer Methods and Programs in Biomedicine},
   title = {Mask_explorer: A tool for exploring brain masks in fMRI group analysis},
   url = {http://ac.els-cdn.com/S0169260716300384/1-s2.0-S0169260716300384-main.pdf?_tid=ba09c964-7b4b-11e6-ab05-00000aab0f26&acdnat=1473947765_fafba2b46869b03f0eec8cf83b288b99},
   volume = {134},
   year = {2016}
}

TY  - JOUR
ID  - 1354130
AU  - Gajdoš, Martin - Mikl, Michal - Mareček, Radek
PY  - 2016
TI  - Mask_explorer: A tool for exploring brain masks in fMRI group analysis
JF  - Computer Methods and Programs in Biomedicine
VL  - 134
IS  - October
SP  - 155-163
EP  - 155-163
PB  - Elsevier Ireland LTD
SN  - 01692607
KW  - fMRI
KW  - Group analysis
KW  - Dataset explorer
KW  - Preprocessing
KW  - Statistical parametric mapping
KW  - Tool
UR  - http://ac.els-cdn.com/S0169260716300384/1-s2.0-S0169260716300384-main.pdf?_tid=ba09c964-7b4b-11e6-ab05-00000aab0f26&acdnat=1473947765_fafba2b46869b03f0eec8cf83b288b99
L2  - http://ac.els-cdn.com/S0169260716300384/1-s2.0-S0169260716300384-main.pdf?_tid=ba09c964-7b4b-11e6-ab05-00000aab0f26&acdnat=1473947765_fafba2b46869b03f0eec8cf83b288b99
N2  - Background and objective: Functional magnetic resonance imaging (fMRI) studies of the human brain are appearing in increasing numbers, providing interesting information about this complex system. Unique information about healthy and diseased brains is inferred using many types of experiments and analyses. In order to obtain reliable information, it is necessary to conduct consistent experiments with large samples of subjects and to involve statistical methods to confirm or reject any tested hypotheses. Group analysis is performed for all voxels within a group mask, i.e. a common space where all of the involved subjects contribute information. To our knowledge, a user-friendly interface with the ability to visualize subject-specific details in a common analysis space did not yet exist. The purpose of our work is to develop and present such interface. Methods: Several pitfalls have to be avoided while preparing fMRI data for group analysis. One such pitfall is spurious non-detection, caused by inferring conclusions in the volume of a group mask that has been corrupted due to a preprocessing failure. We describe a MATLAB toolbox, called the mask_explorer, designed for prevention of this pitfall. Results: The mask_explorer uses a graphical user interface, enables a user-friendly exploration of subject masks and is freely available. It is able to compute subject masks from raw data and create lists of subjects with potentially problematic data. It runs under MATLAB with the widely used SPM toolbox. Moreover, we present several practical examples where the mask_explorer is usefully applied. Conclusions: The mask_explorer is designed to quickly control the quality of the group fMRI analysis volume and to identify specific failures related to preprocessing steps and acquisition. It helps researchers detect subjects with potentially problematic data and consequently enables inspection of the data. (C) 2016 Elsevier Ireland Ltd. All rights reserved.
ER  -

GAJDOŠ, Martin; Michal MIKL a Radek MAREČEK. Mask\_{}explorer: A tool for exploring brain masks in fMRI group analysis. \textit{Computer Methods and Programs in Biomedicine}. Clare: Elsevier Ireland LTD, 2016, roč.~134, October, s.~155-163. ISSN~0169-2607. Dostupné z: https://doi.org/10.1016/j.cmpb.2016.07.015.

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