003 - ATR Brain Database

Detail

Language

English

Title

003

Free Keywords

Spatial-attention task, fMRI

Description

Date

Apr 13, 2016

Last Modified Date

Jul 3, 2017 15:29:59

Created Date

Apr 13, 2016 10:20:42

Contributor

DBI Database Manager (dbi_db)

Item Type

Data

Change Log(History)

Jul 3, 2017	Modified; Index.
Jul 3, 2017	Modified; Index.
Jul 14, 2016	Modified; Rights.
Jun 24, 2016	Modified; Readme, Rights.
Apr 28, 2016	Modified; Index.
Apr 27, 2016	Modified; Readme.
Apr 27, 2016	Modified; Readme.
Apr 27, 2016	Modified; Index.
Apr 25, 2016	Modified; Readme.
Apr 25, 2016	Modified; Free Keywords.
Apr 25, 2016	Modified; Rights, Experimenter.
Apr 13, 2016	Modified; Experimenter.

Data type

Other

Experimenter

Shikauchi M

Ikeda S

Ogawa T

Preview

Data File

003.tar.gz 794927671 bytes (Login User only)

Readme

Data set of Network-BMI Brain Database Project (NBP)
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Instruction to obtain subject information:
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1. download a subject information file (text/excel file) from http://biomark00.atr.jp/modules/xoonips/listitem.php?index_id=179
and check which dataset (fMRI, EEG, fNIRS) you need.

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Instruction to analyze fMRI data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1. download and install SPM 8 from http://www.fil.ion.ucl.ac.uk/spm/software/spm8/
2. select and download single subject data from http://biomark00.atr.jp/modules/xoonips/listitem.php?index_id=180
3-digit number is corresponding to subject ID. Unzip the downloaded file.

3. You can find a file "SSS.tar.gz" (SSS is the subject ID) in a folder "Data_ZZ" (ZZ is integer number). After unzip "SSS.tar.gz" file, you can find five folders, 
"1": 1st-session of SA task (swravol_XXX.nii, XXX:001~297; swmeanavol_001.nii: mean volume image; rp_avol_001.txt: head movement)
"2": 2nd-session of SA task(swravol_XXX.nii, XXX:001~297; swmeanavol_001.nii: mean volume image; rp_avol_001.txt: head movement)
"3": 3rd-session of SA task(swravol_XXX.nii, XXX:001~297; swmeanavol_001.nii: mean volume image; rp_avol_001.txt: head movement)
"4": 4th-session of SA task(swravol_XXX.nii, XXX:001~297; swmeanavol_001.nii: mean volume image; rp_avol_001.txt: head movement)
"rsfmri": 5-min resting-state (swravol_XXX.nii, XXX:001~157; swmeanavol_001.nii: mean volume image; rp_avol_001.txt: head movement)

NOTE: All EPI data were already preprocessed (slice-timing, realignment, coregistration, normalization, and smoothing) by using SPM 8. Structual MRI images (T1-image) were not uploaded to protect privacy of the subject.

4. download and unzip log file from http://biomark00.atr.jp/modules/xoonips/detail.php?item_id=153

5. load a log file, XXX_runY.mat (XXX: subject ID, Y: session number) on MATLAB. You can find a variable "TrigInfo":

TrigInfo
 - triggerTime: scanning trigger (sec). 1st scan is corresponding to "0" sec.
 - mode: instructed color to pay attention. 'Red' or 'Green'.
 - Right: time information of right-attention trials.
   - cue: timing of attention-cue (sec).
   - offset: offset of a trial(sec).
   - start: start timing of a trial (sec).
   - res: response flg (a subject pushed a bottom or not. "1": responded; "0": not responded).
 - keyTime: timing of pushing the bottom (sec).
 - Left: time information of left-attention trials.
   - cue: timing of attention-cue (sec).
   - offset: offset of a trial(sec).
   - start: start timing of a trial (sec).
   - res: response flg (a subject pushed a bottom or not. "1": responded; "0": not responded).
 - Control: time information of control-attention trials.
   - cue: timing of attention-cue (sec).
   - offset: offset of a trial(sec).
   - start: start timing of a trial (sec).
   - res: response flag (a subject pushed a bottom or not. "1": responded; "0": not responded).
 - cond_vec: vector of condition (character, 1x25; R: right, L: left, C: control)


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Instruction to analyze EEG data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1. download and install EEGLAB from http://sccn.ucsd.edu/eeglab/install.html
2. download and unzip EEG-data files and log files from http://biomark00.atr.jp/modules/xoonips/listitem.php?index_id=181
3. You can find files, XXX_task_Y_.set (XXX: subject ID, Y: session number) in the subject number's folder (e.g. 002, 003).
4. You can load '.set' file on MATLAB,
load(filename, '-mat');
5. You can load log file as a variable 'result' (same as fNIRS logfile)

result
 - bar_onset_time: onset time of bar stimulus (msec)
 - bar_tilt: type of stimulus ([Left, Right]; 1: -15 degree, 2: 0 degree, 3: 15 degree)
 - bar_trial_label: stimulus label (1: Left attention, 2: Right attention, 8: control)
 - bar_orientation: angle of bar ('\':-15 degree, '|':0 degree, '/':15 degree)
 - program_onset: timing of stimulus program start (msec)
 - put_secs: timing of button push (msec)
 - keyCodes: types of the keyboard (Enter botton)
 - trial_label: event trigger(8: start trial, 1/2: start attention period(1:Left,2:Right), 16: start resting period)
 - class_label: trial label (1:Left, 2:Right)
 - attention_label: trial label (1:Left, 2:Right)
 - motor_label: not needed to use in this analysis
 - trial_onset_time: onset timing of all trigger
 - PUSH_LIMIT_TIME: 
 - cue_mode: 'guided'
 - cue_color: 'red' or 'green'



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Instruction to analyze fNIRS data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1. download and unzip fNIRS-data files and log files from http://biomark00.atr.jp/modules/xoonips/listitem.php?index_id=182
2. You can find files, XXX_NIRS_task_Y.mat (XXX: subject ID, Y: session number or 'rs':resting state) in the subject number's folder (e.g. 002, 003).
3. You can load '.mat' file on MATLAB, then find a variable "NIRS",
NIRS
 - data: [1x1 struct]
   - mat(49 channels x data points x 6 signals)
   - label: 'OxyHb','DeoxyHb','TotalHb','Abs780nm','Abs805nm','Abs830nm'
 - times: [1x1 struct]
   - data: vector(1 x data points)
   - unit: 'second'
 - event: [1x1 struct]
   - data: vector(1 x data points)
   - label: '16:rest','8:control','2:attention' (NOTE: In the case of 'rs', label is '1:Start recording')
   - count: vector(1 x data points), counting the number of events
 - ch_nirs: [1x49 double]
 - ch_pos: [49x3 double]

4. download and unzip sensor-position file from http://biomark00.atr.jp/modules/xoonips/detail.php?item_id=171
5. In "PosFile" folder, you can find txt-file or mat-file, XXX_pos.txt/XXX_pos.mat(XXX: subject ID). These coordinations are corresponding to positions of EEG electrodes and NIRS probes.


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Reference paper
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
When getting experimental information in detail,please refer to the following paper: 

(1) Hiroshi Morioka, Atsunori Kanemura, Satoshi Morimoto, Taku Yoshioka, Shigeyuki Oba, Motoaki Kawanabe, and Shin Ishii (2014).
Decoding spatial attention by using cortical currents estimated from electroencephalography with near-infrared spectroscopy prior information. NeuroImage 90: 128-139.

(2) Hiroshi Morioka, Atsunori Kanemura, Junichiro Hirayama, Manabu Shikauchi, Takeshi Ogawa, Shigeyuki Ikeda, Motoaki Kawanabe, and Shin Ishii (2015).
Learning a common dictionary for subject-transfer decoding with resting calibration. NeuroImage 111: 167-178.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Feedback & Bug report  
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Any feedback and bug report are welcome. Please contact dababase administrator (dbi_db@atr.jp).

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Acknowledgements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This database is brought to you by ATR Cognitive Mechanisms Laboratories in Kyoto.

Rights

All intellectual property rights of NBP data are reserved by Japan Ministry of Internal Affairs and Communications. 
License:
NBP Data is free but copyright data set, distributed under the terms of ATR NBP User Agreement. First, the ATR NBP User must register from here http://www.cns.atr.jp/dbi/download/

Index

/ Public / mic / SpatialAttention / MRI / Group2

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