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Spatial_mask pipeline

From a list of images resulting from a previous segmentation, produces a grey matter mask

Pipeline insight

• Spatial_mask pipeline combines the following bricks:

  • GM_WM_Normalize

  • Threshold

  • Smooth

  • Resample1

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inputs parameters:

• native_class_images

  A list of images, resulting from a previous segmentation to grey matters, white matters, etc. (valid extensions: [.nii, .nii.gz]).

  ex. ['/home/username/data/raw_data/c1anat.nii',
       '/home/username/data/raw_data/c2anat.nii',
       '/home/username/data/raw_data/c3anat.nii',
       '/home/username/data/raw_data/c4anat.nii',
       '/home/username/data/raw_data/c5anat.nii',
       '/home/username/data/raw_data/c6anat.nii']
  

• deformation_file

  File y_*.nii containing 3 deformation fields for the deformation in x, y and z dimension (a pathlike object or string representing an existing file (valid extensions in [.img, .nii, .hdr]).

  ex. /home/username/data/raw_data/y_anat.nii
  

• smoothed_func

  A functional image (valid extensions: [.nii, .nii.gz]).

  ex. /home/username/data/raw_data/func.nii
  

Outputs parameters:

• mask_003

  The grey matter mask at the resolution of the smoothed_func.

  ex.  /home/username/data/derived_data/mask_swc1anat_003.nii
  

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NOTE:

• The selection of the images is made using the syntax of SPM (c1* for grey matter and c2* for white matter).