I, on behalf of all contributors, would like to announce that three toolboxes are released for free downloading. All of them are Matlab-based, thus unzip and setpath is required (we encourage setpath SPM8, REST, DPARSF as well). For more details please see each toolbox's manual. These software are beta version v1.0, so please feel free to pose any comment, feedback, bug report, suggestions. We will make them better accordingly. I'd like to briefly state the usage of them:
1. ES Calc: Toolbox (effect_size.zip) as well as manual (English version and Chinese version).
Brain imaging result is not only T/Z/F-statistic maps, ES Calc will help you generate effect size map for your report. Effect size has been suggested and encouraged to report to provide a supplementary to statistical analysis. For example, two-sample t-test will tell you whether or not your two groups have statistically "significant" difference in a probablistic fasion (p value), Effect Size, on the other hand, helps you judge the group difference in a more realistic and biological meaningful way (is it "big"? "medium"? or "small"?).
Developers: Zhongzhan GAO (firstname.lastname@example.org) and Xun LI (email@example.com).
2. Decom (Temporal decomposition toolbox, Decom.zip) and its manual (EN and CN).
Our brain is complex, both in spatial and temporal aspects. Decom uses temporal decomposition method (Liu and Duyn2013, PNAS) to decompose the fMRI data into various "modes", or "spatial patterns", each of which occurs in some time points (i.e., frames), rather than lasts throughout the scanning time. For example, if you use the PCC area as seed region and calculate seed-based functional connectivity, you will get a default mode network (DMN). But if you use Decom toolbox, it will generates several networks, including the DMN, visual areas, sensorimotor areas, or executive control network. This means that the brain is not a static, but acts as dynamic system. The PCC, sometimes interacts with DMN, sometimes co-activated with Visual network, and sometimes co-activated with motor network. Decom will tell you which networks temporally interact with your seed, and when.
Developers: Xun LI (firstname.lastname@example.org)
3. TUMOR (Toolbox for fUnctional Mapping preOperatively based on Resting-state fMRI, TUMOR.zip) and manual (currently only Chinese version, will upload EN manual soon).
For many doctors, or neurosurgeons, analyzing fMRI data for presurgical planning (i.e., preoperative functional mapping) is quite laborious, and too many softwares should be used. TUMOR is designed for them. It is a toolbox for mapping the eloquent functional areas (e.g., sensorimotor, langauge) preoperatively based on resting-state fMRI data. If your hospital does not have task stimulation system for MRI, you may need to conduct a resting-state fMRI scan, because it is easier, less-demanding, better cooperation by patients. Resting-state fMRI has been proposed for presurgical planning, so, why not use this toolbox and just after several clicks you will get the results for presurgical planning! It can do seed-based functional connectivity and independent component analysis.
Developers: Huiyuan HUANG (email@example.com)
Liu X, Duyn J H. Time-varying functional network information extracted from brief instances of spontaneous brain activity. Proceedings of the National Academy of Sciences, 2013, 110(11): 4392-4397.
|Manual_Effect size calculator for Brain Imaing_EN.docx||687.23 KB|
|Manual_Temporal Decomposition toolbox_EN.docx||1.12 MB|
|Manual_TUMOR V1.0_EN.pdf||2.64 MB|