This repository contains the code for a MATLAB application for annotating time-points in real-time MRI videos.

Tanner Sorensen
Signal Analysis and Interpretation Laboratory
University of Southern California

Open MATLAB with the desktop GUI. Double click on the file "rtMRI_Timepoints_Annotator.mlappinstall".

Click "Install" in the dialogue box.

The application will appear in the "APPS" tab.

Click on the tab. You will find the application "rtMRI_Timepoints_Annotator" in the dropdown menu.

Click on the "APPS" tab. Open the application "rtMRI_Timepoints_Annotator" in the dropdown menu.

Click on the button "choose directory". Open the directory containing the avi files (see Section "Generating audio-video files for analysis" below).

A list of avi files in the directory appears. Click on the file you want to analyze.

Use the top slider and "current frame" up/down arrows to navigate to the video frame at the start of the time-interval you are interested in. Click "onset" to set the start of the time-interval. navigate to the video frame at the end of the time-interval you are interested in. Click "offset" to set the end of the time-interval.

Click on the "Examine Selection" tab and then the "play" button to review the video and audio from the selected time-interval.

Return to the "Timepoint Annotation" tab. If the selection must be revised, reselect onset and offset time-points. Otherwise, click "add to table" in order to add the time-interval to the table. Label the time-interval by clicking in the cell beneath the column "Label" in the table.

Click "export table" to write the table to csv file.

The application will open real-time MRI videos without interleaved audio, but to fully utilize the application, avi files should have both audio and video streams.

Navigate to the directory containing folders avi and wav that have video and audio files, respectively.

tsorense@tsorense-Precision-WorkStation-T3500:~/Downloads/eh$ ls *
avi:
lac01282018_18_47_25.avi  lac01282018_18_52_37.avi  lac01282018_18_56_27.avi  lac01282018_18_59_45.avi  lac01282018_19_04_20.avi  lac01282018_19_08_57.avi  lac01282018_19_13_49.avi
lac01282018_18_48_58.avi  lac01282018_18_54_00.avi  lac01282018_18_57_39.avi  lac01282018_19_00_53.avi  lac01282018_19_05_46.avi  lac01282018_19_10_48.avi  lac01282018_19_14_49.avi
lac01282018_18_51_14.avi  lac01282018_18_55_08.avi  lac01282018_18_58_46.avi  lac01282018_19_02_16.avi  lac01282018_19_07_16.avi  lac01282018_19_12_09.avi

wav:
lac01282018_18_47_25.wav  lac01282018_18_52_37.wav  lac01282018_18_56_27.wav  lac01282018_18_59_45.wav  lac01282018_19_04_20.wav  lac01282018_19_08_57.wav  lac01282018_19_13_49.wav
lac01282018_18_48_58.wav  lac01282018_18_54_00.wav  lac01282018_18_57_39.wav  lac01282018_19_00_53.wav  lac01282018_19_05_46.wav  lac01282018_19_10_48.wav  lac01282018_19_14_49.wav
lac01282018_18_51_14.wav  lac01282018_18_55_08.wav  lac01282018_18_58_46.wav  lac01282018_19_02_16.wav  lac01282018_19_07_16.wav  lac01282018_19_12_09.wav

Combine the audio and video files using the following commands.

tsorense@tsorense-Precision-WorkStation-T3500:~/Downloads/eh$ mkdir avi_withaudio; for i in $(ls avi); do ffmpeg -i "avi/$i" -i "wav/${i/.avi/.wav}" -c copy "avi_withaudio/$i"; done

This produces a directory avi_withaudio, containing the avi files with both audio and video streams.

tsorense@tsorense-Precision-WorkStation-T3500:~/Downloads/eh$ ls avi_withaudio/
lac01282018_18_47_25.avi  lac01282018_18_52_37.avi  lac01282018_18_56_27.avi  lac01282018_18_59_45.avi  lac01282018_19_04_20.avi  lac01282018_19_08_57.avi  lac01282018_19_13_49.avi
lac01282018_18_48_58.avi  lac01282018_18_54_00.avi  lac01282018_18_57_39.avi  lac01282018_19_00_53.avi  lac01282018_19_05_46.avi  lac01282018_19_10_48.avi  lac01282018_19_14_49.avi
lac01282018_18_51_14.avi  lac01282018_18_55_08.avi  lac01282018_18_58_46.avi  lac01282018_19_02_16.avi  lac01282018_19_07_16.avi  lac01282018_19_12_09.avi

If you are using a version of MATLAB older than 2018a, a dialogue box may appear indicating that the application was built on a newer version of MATLAB. Malfunction of the application may in this case might be resolved by upgrading MATLAB to the latest version.

Low-level graphics errors can occur. MATLAB has a page of documentation for solving these issues (link). If the graphics card is old, one solution is to switch to rendering with Software OpenGL.