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nipreps / mriqc-learn

Learning on MRIQC-generated image quality metrics (IQMs).
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How to save output .csv file from mriqc_clf in directory of choice (using Singularity)? #9

Open JohannesWiesner opened 3 years ago

JohannesWiesner commented 3 years ago

I would like to use MRIQC's classifier to classify my T1 raw data. For that I used the following lines of code:

singularity exec -H /local/path/to/dir/of/my/choice \
-B /local/path/to/output/:/output \
/path/to/singularity_file/mriqc_latest.sif mriqc_clf --load-classifier -X /output/group_T1w.tsv -v

This works fine and I get my .csv file, however, the output .csv file is stored within the working directory of the shell from which this code was executed. If I leave away -H /path/to/dir/of/my/choice, the .csv file is simply stored in my local home directory (/home/johannes.wiesner/mclf_run-20210310-150418*).

However, I would like to be able a path to specify where exactly to store it. Is there such an option? It seems like in earlier day there was a -o flag that was supposed to handle this? I cannot find any documentation on how to do this, or maybe there is simply no solution for it?

This issue seems to be related to nipreps/mriqc#699 ?

oesteban commented 2 years ago

The MRIQC classifier aged pretty badly. We have outsourced it to the nipreps/mriqc-learn package, where I'm also moving this issue for reference.