NIfTI (Neuroimaging Informatics Technology Initiative) Reader Parameters

Dataset Parameters

This parameter allows you to choose different naming schemes, and the number of feature types generated for the reader.

Feature type name choices:

  • From Format Name: Produces only a single feature type containing the format name.
  • From File Name(s): Generates one feature type per source filename.

Schema Attributes

Additional Attributes to Expose

Use this parameter to expose Format Attributes in FME Workbench when you create a workspace:

  • In a dynamic scenario, it means these attributes can be passed to the output dataset at runtime.
  • In a non-dynamic scenario, this parameter allows you to expose additional attributes on multiple feature types. Click the browse button to view the available format attributes (which are different for each format) for the reader.
 

Use Search Envelope

A search envelope (also known as a bounding box) is a rectangular area that defines a geographic area. In FME, the easiest way to define a search envelope is to use search envelope parameters.

Defining a search envelope is the most efficient method of selecting an area of interest because FME will read only the data that is necessary – it does not have to read an entire dataset. Search Envelope parameters apply to both vector and raster datasets and can be particularly efficient if the source format has a spatial index.

Most FME readers have parameters to define the search envelope of data that is being read:

Screenshot with blank search envelope min and max x and y parameters

The parameters include the x and y coordinates of the bounding box as well as a parameter that defines the coordinate system.

How to Define the Bounding Box

Using the minimum and maximum x and y parameters, define a bounding box that will be used to filter the input features. Only features that intersect with the bounding box are returned. Note that the bounding box intersection is not a full geometry intersection (based on spatial relationships) that would be returned by a transformer like the SpatialFilter.

Note  If all four coordinates of the search envelope are left at 0, the search envelope will be disabled even if this option is checked.

Search Envelope Coordinate System

Specifies the coordinate system of the search envelope if it is different than the coordinate system of the data. The coordinate system associated with the data to be read must always be set if this parameter is set.

If this parameter is set, the minimum and maximum points of the search envelope are reprojected from the Search Envelope Coordinate System to the reader’s coordinate system prior to applying the envelope.

Clip to Search Envelope

The underlying function for Use Search Envelope is an intersection; however, when Clip to Search Envelope is checked, a clipping operation is also performed.

  • When left unchecked (set to No), features that overlap the boundary will be included in their full (unclipped) form.
  • When checked (set to Yes), this option instructs FME to clip features to the exact envelope boundary. FME removes any portions of imported features being read that are outside the search envelope.

Clip to Search Envelope: No

Clip to Search Envelope: Yes

Any features that cross the search envelope boundary will be read, including the portion that lies outside of the boundary.

Any features that cross the search envelope boundary will be clipped at the boundary, and only the portion that lies inside the boundary will be read.

The search envelope includes the bounding box and the extent of the raster.

The search envelope includes only the area within the bounding box.

The raster size will still match the bounding box, but the area without data will be filled with Nodata values to represent the absence of data, if the source raster has them.

Raster Nodata may be a single value across all bands, a single value per band, or a separate alpha or transparency band that indicates the lack of data values (this is more common in images than other types of rasters).

Transformation Matrix

NIfTI files come with an affine transformation that maps pixel locations to a coordinate system. This parameter controls whether or not the NIfTI reader will honor the transformation. This transformation contains important spatial information, and discarding it may result in left and right being inverted.

Option

Description

Apply

This option represents points in the intended location in the described coordinate system. It requires resampling, which introduces error. Pixels sampled outside the original solid will be set to 0.

The raster slices will be xy-aligned, with the x and y axes of the coordinate system mapped by the transformation. A z coordinate is specified as an attribute.

When this option is enabled, the x and y values of a point on the raster slice correspond to the intended x and y coordinates of that point in the space described by the NIfTI file. The z coordinate of point on the raster is indicated by the nifti_z_coordinate attribute of the raster to which it belongs.

Discard

The reader will ignore the transformation contained in the NIfTI file and produce raster slices from the raw grid of pixel values.

This is the fastest option and in some cases produces visually reasonable results, but important information might be lost.

Interpolation Type

Rasters may need to be resampled to different sizes during writing. This option specifies how cell values should be interpolated:

  • Nearest Neighbor is the fastest but produces the poorest image quality.
  • Linear provides a reasonable balance of speed and quality.