FitLins HTML summary reports missing statistical ouputs

Summary of what happened:

Hi all - I’ve successfully run FitLins (via Docker) on my own data and it creates the expected output. When I examine the model-*.html report all the images are missing. I established that this was partly down to the mapping of folders between the Docker container and my local folders and a simple sed command solved all that. But then I realised that only applied to some of the images - the contrast maps did not display. Closer examination of the html showed that they weren’t even included, yet the .png files are all present in their respective figures folders. In the contrasts sections of the report, there is simply the message:

Missing contrast skipped (used: --drop-missing )

Anyone else experienced this and know of a workaround? Thanks!

Shell script for running FitLins:



docker run --rm -it \
    -v ${BIDSdir}:/bids:ro \
    -v ${BIDSdir}/derivatives:/prep:ro \
    -v /Volumes/Cortex/BIDS/analysed:/out \
    -v /Volumes/Cortex/fitLins:/scratch \
  poldracklab/fitlins:latest \
    -v \
    -m /bids/code/${model_file} \
    -d /prep \
    -w /scratch \
    --space MNI152NLin2009cAsym \
    --desc-label preproc \
    --estimator nilearn \
    --drift-model cosine \
    --smoothing 8:run:iso \
    /bids /out dataset

input_file=$(find /Volumes/Cortex/BIDS/analysed -type f -name 'model-*.html')
sed -i.bak 's/\/out\//\/Volumes\/Cortex\/BIDS\/analysed\//g' "$input_file"

I’ve realised that somebody else raised this same issue recently, so it seems its not specific to me!
@sajjad Did you get any luck resolving the issue?

OK - I think my last post on this issue - I seem to be answering my own questions :crazy_face:

Seems this issue has also been raised on the FitLins GitHub too and is still open. Lets hope there will be an updated version release soon?


Thanks for the bug report.

The team is traveling to conferences right now but hopefully we can take tackle this issue in July.


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