brainlife/app-slicer-fsl

app-slicer-fsl

app-slicer-fsl's Issues

image.json missing

This App uses "images" datatype for the output, but it doesn't generate the output in a correct data structure.

All images should be stored under "images" subdirectories, and there should be images.json which describes stored image.

So the output (raw) directory should look like this.

Alternatively, this App could just store the output image in base64 encoded .png as part of product.json (like app-hcp-acpc-alignment App).

# make png
some_command input.data -o out.png

# create product.json
cat << EOF > product.json
{
    "brainlife": [
        { 
            "type": "image/png", 
            "name": "Alignment Check (-x 0.5)",
            "base64": "$(base64 -w 0 out.png)"
        }
    ]
}
EOF

If we do this, a user won't have to open anything to view the image - it will be display as part of the task output.

Don't need raw output?

I believe it's better to just show the output image as part of product.json - and not even bother generating and output datatype.

So, at the end of main

cat << EOF > product.json
{
    "brainlife": [
        {
            "type": "image/png",
	    "name": "mid-axial, sagittal, and coronal",
            "base64": "$(base64 -w 0 raw/output.png)"
        }
    ]
}
EOF

Actually, the the bigger question might be.. do we still need this App now that anat/t1w validator generates the sliced png for all t1w?