MouseMove Troubles

Hey guys,

I’m an undergraduate student working in a neuroscience lab that is interested in using an ImageJ plugin associated with MouseMove seen: here. We have the most updated version of Fiji (ImageJ), as shown here.

We also have the requisite stackreg and turboreg plugins in the plugin folder, and the preprocessing macro located in the macro folder.

This program uses two videos to generate a .txt with relevant data to rodent tracking, which is later processed by MouseMove.exe. However, we have yet to get this far.

We have rendered the two supplementary videos used to test the preprocessor into the correct frame rate, and size using the online converter found: here. We then used the ffmpeg command"ffmpeg -i infile.avi -pix_fmt nv12 -f avi -vcodec rawvideo outfile.avi" found here to obtain the necessary compression for ImageJ to run the files.

Upon running the macro, the log reads:

Start batch preprocessing…
All files in the directory are completed!

This is the end message programmed into the preprocessing macro, the output of which should be a file with the name Tkresults_mouse.txt – however, a total computer search does not yield this text file. This suggests that all though the log indicates that the program was completed, and no errors were given, that the preprocessing macro still failed to produce the necessary .txt file for MouseMove.exe to interpret.

I’ve been working on this for nearly ten hours. I tried contacting the corresponding author, but have yet to receive a reply.

I am hoping that someone might see what the issue is, and be able to offer some advice. I very much appreciate any help.

Thank you,

Update: I have also tried the example videos provided by the corresponding Author on their ResearchGate page. They are both in avi format to start with, and should, hypothetically, not require any processing. Instead of the macro completing for this set of videos, however, I receive the error: “Unrecognized command: Stackreg,” despite Stackreg and Turboreg both being located in the plugin folder (and despite receiving an error free completion message in the log when using the videos we processed into the correct format ourselves.)

Dear @srztanjur,

I quickly looked at the preprocessing macro. Does the folder that you select contain any files? If so, do the file names fit the required scheme (that I hope is described in the publication)? The macro seems to check if the filename contains the term empty and only in that case does some preprocessing.

In cases where the macro is in the supplementary materials, your best chance really is to contact the corresponding authors. If you solve the issue somehow, it would be really great to report back here so that anyone with a similar issue can find the solution out in the open :wink:


Note that this question was cross-posted to the ImageJ mailing list.

I receive the error: “Unrecognized command: Stackreg,” despite Stackreg and Turboreg both being located in the plugin folder

The correct way to install StackReg into Fiji is to enable the BIG-EPFL update site, rather than attempting to install the plugins manually.

Looking at the Preprocessing.ijm source code, there are many more print statements throughout the code, while looping over each file in the chosen directory. Since no such messages are being printed, it suggests that no files in your directory are being selected for processing.

Looking in more detail at the code, we see these lines:

if (ix>0)//Check whether this is a background video

So if a filename does not have the string empty somewhere in it, it is skipped. Do your files contain the string empty in their names?

Taking a step back: for many reasons, I do not think MouseMove is a good tool for end users. It is an all-too-common example of a fragile and convoluted plugin which is not appropriately distributed, licensed, tested or maintained.

Are you certain you need this specific program to perform your specific analysis? I would encourage you to instead describe what you want to achieve scientifically, to start a discussion regarding the best way forward.