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brainlife / app-mrtrix3-preproc

Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.
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Alignment QC image #9

Open soichih opened 5 years ago

soichih commented 5 years ago

Upon the successful completion of this App, we could generate a simple QC image that shows how well the t1 and preprocessed dwi aligns. Similar to http://nipy.org/dipy/examples_built/affine_registration_3d.html

Just as a reference.. the app-hcp-acpc-alignment does the following to generate the QC image.

# make png
slicer out.nii.gz -x 0.5 out_aligncheck.png

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

https://github.com/brain-life/app-hcp-acpc-alignment/blob/master/run.sh

For mrtrix3 preproc, however, we need to overlay preprocesed dwi on top of t1 (and take affine/sform into consideration?)

Another thing to consider is to auto-scale the dwi image so that it can show enough detail to see if it properly aligns with t1.

bacaron commented 4 years ago

Coming back to this. Soichi i'm working on a few slicer apps, including one for the overlay of the DWI/T1 image. Unfortunately, there's going to be an issue with differences in file sizes between the DWI and T1. I'm not sure how to get around this at this point.

soichih commented 4 years ago

I thought the output dwi should have the same size as the input t1 that dwi is registered to?