unravel.register.adjust_template module#

Use reg_adjust_template (rat) from UNRAVEL to adjust intensities in a template for a single set of atlas label IDs.

Note

  • The boundary between the adjusted region and the rest of the image can be sharp or blurred by applying a Gaussian blur to a two-sided boundary band around the region.

  • The boundary band is computed as:

    inside band = region - erosion(region, band_width) outside band = dilation(region, band_width) - region band = inside OR outside

  • We blur the full (modified) image, then replace only band voxels with blurred values.

Example of use (separate steps):#

# 1) Fiber tracts: scale by 0.85 reg_adjust_template -i template.nii.gz -a atlas.nii.gz -ids <FIBER_IDS…> –scale 0.85 -bb -o template_fibers.nii.gz

# 2) HPF: scale by 0.8 (using previous output) reg_adjust_template -i template_fibers.nii.gz -a atlas.nii.gz -ids <HPF_IDS…> –scale 0.8 -bb -o template_fibers_hpf.nii.gz

# 3) DG/CAsp: scale by 2.0 (using previous output) reg_adjust_template -i template_fibers_hpf.nii.gz -a atlas.nii.gz -ids <DG_CAsp_IDS…> –scale 2.0 -bb -o template_fibers_hpf_dg.nii.gz

Usage:#

reg_adjust_template -i path/image.nii.gz -a path/atlas_labels.nii.gz -ids <ID1> <ID2> … -o path/output.nii.gz [–scale <factor> | –set <value>] [-bb -s <float> -bw <int>] [-dt <dtype>] [-v]

unravel.register.adjust_template.parse_args()[source]#
unravel.register.adjust_template.mask_from_ids(atlas, ids)[source]#

Binary mask where atlas label is in ids.

Parameters:

  • atlas (ndarray) –

  • ids (list[int]) –

Return type:

ndarray

unravel.register.adjust_template.boundary_band_mask(region_mask, band_width=1)[source]#
Two-sided boundary band:

inside band = region - erode(region, n) outside band = dilate(region, n) - region band = inside OR outside

Parameters:

  • region_mask (ndarray) –

  • band_width (int) –

Return type:

ndarray

unravel.register.adjust_template.safe_cast_like(x, dtype)[source]#

Cast with rounding/clipping if integer.

Parameters:

  • x (ndarray) –

  • dtype (dtype) –

Return type:

ndarray

unravel.register.adjust_template.main()[source]#