CONN GUI crashed (not responding) and the connproject.mat file was corrupted

Hi there,

I’m using CONN GUI to process 300+ rs-fmri data, however, the GUI screen crashed while performing on “checking if data files have been edited or move, press cancel to skip this step” for multiple hours. (The mouse can still move but it’s not responding anymore) It happened several times before, last time I had to close by entering tty and kill Matlab. And when I reopened CONN GUI and loaded the project, it turns out that all the steps that I’ve been performed (preprocesssing, denoising, 1st and 2nd level analysis) were gone in the GUI panel. However, I did perform “project → save” before it got crashed. The processed images are still intact in the CONN project folder, but the connproject.mat somehow got corrupted and cannot link the CONN GUI to the steps that’s been processed before.

I was wondering if there is any way to kill the process while it got stuck but still safely save the connproject.mat? Or if there is any way to save the corrupted connproject.mat, so I don’t have to process all the steps that I’ve been performed again?

Many thanks in advance!


So the MATLAB save command used in conn can only save up to a certain file size. Chances are with 300+ files that it exceeds it. If you go into the conn MATLAB source code, you can add an argument to the save command to allow you to save larger files. I can try to find it and get back to you.


You would have to add ‘v7.3’ to the save command to deal with large files. If you want I can send you the modified conn.m script that has this included. Please send me a DM with your email if you want it.


Also, this will not impact the saving time, it will still take a while. May I suggest alternatives that scale better for large datasets, like post processing your data with and then putting resultant images in a Nilearn glm to run your connectivity analyses?