[Atlas] Hierarchy Tools

• Convert hierarchy formats (hie, csv, xls...) ;
• Simplify hierarchies (i.e., extract a subhierarchy from a more complex hierarchy).

For now, only conversions between hie and csv are possible.

Description

Table inputs (csv or xls) should be of the following format :

Region	Level 1	Level 2	Level 3	Level 4	Level 5	Label	Abbreviation	Color
csf	intracranial					1	CSF	191;192;212
ventricles	intracranial	csf				2	LV	121;117;116
medulla	intracranial	brain	hindbrain			3	Md	147;90;125
pons	intracranial	brain	hindbrain			4	Pn	196;169;176
cerebellum	intracranial	brain	hindbrain			5	Cb	146;139;113
etc.

• Columns name and order can be of the user choice ;
• There should be one line for each region associated with a label value, a color or an abbreviation. In this case, a "name" or "id" column is mandatory ;
• Level columns are mandatory for a true hierarchical labelling ;
• If, for some lines, some of the level columns are unused (i.e. the node depth is less than the max depth), they can either be left blank or filled with the deepest necessary level (but not the name level if a "name" column is provided) ;
• Color must be provided as RGB in any vector form : 200;150;250 or (200,150,250) or [200;150;250], etc.

Parameters

Input_Hierarchy: Text file ( input )

Input hierarchy to convert or simplify.

Input_Atlas: 3D Volume ( optional, input )

Volume of atlas labels corresponding to the input hierarchy. If the process is used to simplify a hierarchy, a simplified volume with merged labels can be genrerated.

Name_Key: OpenChoice ( optional, input )

If the input is a table (csv, xls), the column name (or number) that corresponds to the region name.

Label_Key: OpenChoice ( optional, input )

If the input is a table (csv, xls), the column name (or number) that corresponds to the region label (i.e. integer values in the volume of labels).

Color_Key: OpenChoice ( optional, input )

If the input is a table (csv, xls), the column name (or number) that corresponds to the region color. It will be stored in the output hierarchy so that graphes can be automatically colored in Anatomist.

Abr_Key: OpenChoice ( optional, input )

If the input is a table (csv, xls), the column name (or number) that corresponds to the region abbreviated name. For now, it is kept if the ouput hierarchy is a table (csv, xls), but nothing is done with it anyway.

Id_Key: OpenChoice ( optional, input )

If the input is a table (csv, xls), the column name (or number) that corresponds to the region unique identifier. For now, it is kept if the ouput hierarchy is a table (csv, xls), but nothing is done with it anyway.

Level_Keys: ListOf( OpenChoice ) ( optional, input )

If the input is a table (csv, xls), the column name (or number) that corresponds to the different hierarchy levels. They should be ordered by ascending depth.

Select_Regions: ListOf( OpenChoice ) ( optional, input )

Select region nodes that should be kept in the output hierarchy. If none are provided, the full hierarchy is kept as is. Else, only selected nodes will be kept and labels will be merged accordingly.

Select_Palette: Choice ( optional, input )

Load a palette for the automatic coloring of graph nodes. It should be a 1D color image (i.e. dimensions Y, Z, T should be 1).

Palette: 2D Image ( optional, input )

Output_Hierarchy: Text file ( optional, output )

Output converted hierarchy.

Output_Atlas: 3D Volume ( optional, output )

Output volume of atlas labels, with labels merged so that they correspond with the new merged hierarchy.

Technical information

Toolbox : Primatologist

User level : 0

Identifier : AtlasHierarchyTools

File name : brainvisa/toolboxes/primatologist/processes/atlases/AtlasHierarchyTools.py

Supported file formats :

Input_Hierarchy :

Hierarchy, CSV file, Hierarchy, XLS file, XLSX file

Input_Atlas :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

Palette :

gz compressed NIFTI-1 image, Aperio svs, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIF image, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, VIDA image, Ventana bif, XBM image, XPM image, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

Output_Hierarchy :

Hierarchy, CSV file, Hierarchy, XLS file, XLSX file

Output_Atlas :

gz compressed NIFTI-1 image, BMP image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIF image, GIS image, JPEG image, MINC image, NIFTI-1 image, PBM image, PGM image, PNG image, PPM image, SPM image, TIFF image, TIFF(.tif) image, VIDA image, XBM image, XPM image, gz compressed MINC image, gz compressed NIFTI-1 image