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Anat_headmask pipeline

Compute head mask from skull stripped structural image using Denoise from Dipy

  • Adapted from mriqc anatomical workflow.

Pipeline insight

Anat_headmask pipeline combines the following pipelines and processes:
- Estimate SNR
- Enhance
- Denoise
- Gradient Threshold
Anat headmask pipeline

Mandatory inputs parameters

  • in_file (a string representing an existing file)

    Skull stripped anatomical image (T1w or T2w) (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/ss_T1w.nii'
  • seg_file (a string representing an existing file)

    Segmented image of the in_file (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/ss_T1w_seg.nii'

Outputs parameters:

  • out_file

    Head mask.

    ex. '/home/username/data/derived_data/denoise_ss_T1w_enh_grad.nii'

Useful links:

mriqc