hipsta.run_hipsta

hipsta.run_hipsta(filename, hemi, lut, outputdir, **kwargs)

Run the hippocampal shape and thickness analysis

Parameters:

filename

Filename of a segmentation file.

hemi

Hemisphere. Either ‘lh’ or ‘rh’.

lut

Look-up table: a text file with numeric and verbal segmentation labels. ‘freesurfer’, ‘ashs-penn_abc_3t_t2’ and ‘ashs-umcutrecht_7t’ are keywords for built-in tables.

outputdir

Directory where the results will be written.

no_cleanupoptional

Keep files that may be useful for diagnostic or debugging purposes, but are not necessary otherwise. Default: False

no_cropoptional

Do not crop image. Default: False.

upsampleoptional

Upsample to the smallest voxel edge length. Default: False

upsample_sizeoptional

Upsampling factors. Should be between 0 and 1. If all zeros, upsample to the smallest voxel edge length. Default: [0, 0, 0]

no_merge_molecular_layeroptional

Do not merge molecular layer (only applicable for FreeSurfer segmentations). Default: False

automask_headoptional

Automated boundary detection for hippocampal head. Default: False

automask_tailoptional

Automated boundary detection for hippocampal tail. Default: False

automask_head_marginoptional

Margin for automated boundary detection for hippocampal head. Default: 0

automask_tail_marginoptional

Margin for automated boundary detection for hippocampal tail. Default: 0

no_gauss_filteroptional

Do not apply gaussian filter. Default: False

gauss_filter_sizeoptional

Filter width and threshold for gaussian filtering. Default: [1, 50]

long_filteroptional

Apply filter along longitudinal axis, i.e. attempt to create smooth transitions between slices. Default: False

long_filter_sizeoptional

Size of longitudinal filter. Default: 5

no_close_maskoptional

Do not apply closing operation to mask, i.e. do not attempt to close small holes. Default: False

mcaoptional

Type of marching-cube algorithm. Either ‘mri_mc’ or ‘skimage’. Default: ‘mri_mc’

remeshoptional

Apply remeshing operation to surface, i.e. create a regular, evenly spaced surface grid. Default: False

smoothoptional

Mesh smoothing iterations. Default: 5

cut_rangeoptional

Range for tetrahedral boundary cutting. Default: [-0.975, 0.975]

aniso_alphaoptional

Anisotropy parameter(s). Can be one or two numbers. Default: [40]

aniso_smoothoptional

Anisotropy smoothing iterations parameter. Default: 3

thickness_gridoptional

Extent and resolution of the grid used for thickness computation; three lists of three numbers: negative extent of x axis, positive extent of x axis, resolution on x axis. Repeat for the y and z axes. Default: [ -0.9, 0.9, 41, -0.975, 0.975, 21, -0.9, 0.9, 11]

mccoptional

Marching-cube connectivity. Only used for ‘mri_mc’ algorithm. Default: 1

remesh_sizeoptional

Target number of vertices for remeshing operation. If zero, keep original number of vertices. Default: 0

no_check_surfaceoptional

Do not check surface and proceed if there are holes. Default: False

no_check_boundariesoptional

Do not check boundaries and proceed if there are less / more than two continuous boundary loops. Default: False

no_qcoptional

Do not perform QC. Default: False

allow_ragged_surfaces

Allow ragged mid-surfaces. Default: False

allow_ragged_trias

Allow triangles for ragged mid-surfaces. Default: False

no_orientoptional

Do not orient surfaces. Default: False

Returns:

dict

a dictionary of input arguments