Any way to generate the HTML reports after preprocessing has already completed?



I recently preprocessed a dataset using fmriprep but, because of a computer issue, it ended prematurely. All of my files are present and look fine but I’m missing the HTML reports. I find these very helpful for visually troubleshooting each preprocessing step, so I was wondering if there is any way to generate these after the fact. Thanks!


If you still have the working directory, you can re-run with --reports-only to aggregate the reports. It is also safe to simply repeat the fmriprep command; if all steps finished correctly, it will simply check that the output directory hasn’t changed, and then construct the reports. (This might take a minute or two, depending on the size of your dataset, but it will also make sure that there aren’t unfinished steps that you failed to notice.)

If you do not still have the working directory, you’ll unfortunately need to rerun. Most, if not all, of the sub-reports require files from the working directory to reconstruct, and the sub-reports are stored in the working directory until they are aggregated into the output directory.


Thanks for the quick response. Unfortunately looks like I’ll have to rerun to get the reports, but now I know.