Depending on your project needs, you can disable the following procedures in
desktop mode for Matlab sessions, disabled by default (MAIN_MATLAB_STARTUP_OPTIONS, etc. flags)
real-time quality assessment (USE_RTQA flag)
incremental GLM (USE_IGLM flag)
region of interest visualization (USE_ROI flag)
Matlab helper session for DCM feedback type, disabled by default (USE_MATLAB_MODEL_HELPER flag)
Initialize and/or Run Matlab Sessions¶
There are two ways to run the required MATLAB sessions:
from a Terminal before starting OpenNFT and pressing the
This mode of shared Matlab sessions allows re-using them after closing and re-starting OpenNFT, which is of benefit for software developments and debugging.
If Matlab sessions are started separately, by pressing the
Initialize button, OpenNFT acknowledges them automatically.
After the Initialization you can choose the Configuration file (*.ini) of the Experiment. This file contains editable parameters, which you need to justify before pressing the
Configuration files (.ini) and Experimental protocols (.json) can be found in /opennft/configs/. Demo data can be found releases. Video Tutorials can be found tutorials. Although Video tutorials were made for an initial upload in 2017 and have somewhat different GUI, the general rationale is preserved (updates are pending).
If you run OpenNFT in offline mode - enable
More about testing OpenNFT on different data is on Testing OpenNFT page.
rtQA mode button is enabled, you can check available quality assessment modes and parameters during data acquisitions.
Start either start data processing in
Offline mode, or waits for fMRI data export from the Scanner otherwise. See tutorials.
During data acquisitions you can change:
View Modes: mosaic, triplanar anatomy, triplanar EPI
Positive and negative statistical maps (not yet available in rtQA mode) and their thresholds
Stop and Exit¶
To stop scanning process press
Stop button. All data will be saved to /Your/Data/Path/NF_Data_1
After exit, all MATLAB sessions will be terminated if they were cd ..
not initialized using the
run_matlab command. Otherwise, use ‘Crtl+C’ in the Terminal to stop them.