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:
BIDSdir=/Volumes/Cortex/BIDS/vEAR
model_file=model-default_smdl.json
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"
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