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

jeffreyallenbrooks · November 7, 2017, 5:09pm

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!

effigies · November 7, 2017, 6:42pm

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.

jeffreyallenbrooks · November 8, 2017, 4:38pm

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

Rubina · July 3, 2021, 8:45am

Hi,

I ran into a similar issue. I recently preprocessed some data (I skipped bids validator because of absent .tsv file atm) using fmriprep but when I opened the visual report I get this:

In the visual reports, I don’t see screenshots of the brain mask, brain tissue segmentation of T1w, EPI to T1 registration and BOLD Summary.

Did I miss something?

Thank you for your help.

Best,

Rubina

effigies · July 8, 2021, 3:53am

You’re looking at an HTML snippet, not the full report. Look for sub-A0123061.html at the root of your output directory (here, it should be C:/Users/rubin/derivatives/fmriprep/sub-A0123061.html).

Rubina · July 8, 2021, 10:12am

Hi @effigies,

Thank you for pointing that out.

I had to change the code a little bit and then it worked and I get this output. Can I ask you for your help again? I got some output files but I could really use a second opinion to see if these files are okay or if something is missing:

Thank you for your help and time.

Best,

Rubina