Command line

patch-denoise minimally requires a path to a NIfTI file, but it can take advantage of reconstructed phase data and/or noise volumes.

Using patch-denoise on BIDS data

Warning

These examples assume that the phase data are in radians. If they are in arbitrary units, you will need to rescale them before running patch-denoise.

Magnitude only

patch-denoise \
    sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
    sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
    --mask auto \
    --method optimal-fro \
    --patch-shape 11 \
    --patch-overlap 5 \
    --recombination weighted \
    --mask-threshold 1

Magnitude with noise volumes

patch-denoise \
    sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
    sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
    --noise-map sub-01/func/sub-01_task-rest_part-mag_noRF.nii.gz \
    --mask auto \
    --method optimal-fro \
    --patch-shape 11 \
    --patch-overlap 5 \
    --recombination weighted \
    --mask-threshold 1

Magnitude and phase

patch-denoise \
    sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
    sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
    --input-phase sub-01/func/sub-01_task-rest_part-phase_bold.nii.gz \
    --mask auto \
    --method optimal-fro \
    --patch-shape 11 \
    --patch-overlap 5 \
    --recombination weighted \
    --mask-threshold 1

Magnitude and phase with noise volumes

patch-denoise \
    sub-01/func/sub-01_task-rest_part-mag_bold.nii.gz \
    sub-01_task-rest_part-mag_desc-denoised_bold.nii.gz \
    --input-phase sub-01/func/sub-01_task-rest_part-phase_bold.nii.gz \
    --noise-map sub-01/func/sub-01_task-rest_part-mag_noRF.nii.gz \
    --noise-map-phase sub-01/func/sub-01_task-rest_part-phase_noRF.nii.gz \
    --mask auto \
    --method optimal-fro \
    --patch-shape 11 \
    --patch-overlap 5 \
    --recombination weighted \
    --mask-threshold 1