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examples doc
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Jenny Chen authored and Jenny Chen committed Aug 27, 2024
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Expand Up @@ -113,10 +113,6 @@ nyudiffusionmri/designer2:<tag> tmi \

The below example mounts the host_path (`/path/to/folder/with/dataset`) to the container_path (`/mnt`). The host_path contains the input series `dwi.mif`. The following is an example that calls tmi and will extract DKI maps with outlier correction and nonlocal means smoothing:
```
pa=/mnt/rpe_b0.nii
dwi=/mnt/dwi.nii
dwi_out=/mnt/dwi_designer.nii
singularity run --bind /path/to/folder/with/dataset:/mnt \
designer2_<tag>.sif tmi \
-DKI -akc_outliers -fit_smoothing 10 /mnt/dwi.mif /data/parameters
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