Image Formats tab

Note: The General options dialog can be displayed by selecting General options on the Options menu.

nordicICE automatically treats any image apart from NifTI format images as a DICOM image and attempts to render it based on the header information. If the file is not recognized as a valid DICOM file, the image is attempted to be read as a RAW image. RAW images are defined as images with no header information where each file only consists of a string of pixel values or any proprietary image format. nordicICE will attempt to extract the pixel data without interpreting any header information. By default, nordicICE will attempt to determine the RAW image format automatically. This can be overridden by setting the appropriate options in this dialog. The voxel size for raw images can also be set here. This is useful if e.g. raw images are to be saved as NifTI images or raw images need to be correctly displayed as MPRs or MIPs.

Raw Image Format

Read as mutli-slice/frame:

Interpret the data as multi-dimensional (mutli-slice or multi-frame) raw images.

Determine format automatically:

When checked the image format is determined automatically by assuming 16 bits/pixel and matrix size to be 2^N (N being an integer greater or equal to 4). This option assumes a single slice image (Partitions=1, Scans/partition=1).

Pixel Offset:

Number of bytes from start of file to first image pixel (i.e. image header size).

Offset betwen slices:

Additional offset (in bytes) between individual slices in a volume

Width/Height:

This specifies the number of pixels in the x and y direction. If the 'Determine automatically' box is checked (default) only images with equal numbers of pixels in the X- and Y- direction are supported.

Partitions:

Number of partitions (slices) (NB: only for multi-sectional (multi-slice) raw files).

Scans/Partition:

Number of images/scans per partition (NB only for multi-sectional raw files).

Flip images:

Flip the images up/down

Raw Pixel Format

16-bits unsigned:

16 bits per pixel but only positive values supported

16-bits signed:

16 bits per pixel with positive and negative values supported.

8-bits:

8 bits per pixel

Swap High/Low order byte:

When checked, the position of the high and low order byte in each 16-bpp pixel. This is sometimes necessary e.g. when importing images from a UNIX based system. Note that in DICOM images any conversion is automatically taken care of.

NIfTI image scaling:

Scale floating point data:

Scale down all floating point data sets. If not checked only series whose max intensity value is beyond the maximum "short integer" allowed are scaled down.

Upper scale limit:

Max intensity value in scaled down image series.

Max:

Set the upper scale limit to its maximum value, i.e. the maximum "short integer".

Max pixel limit:

Scale down series whose max intensity value is below this limit.

Pixel Scaling

Min / Max:

Manually set the maximum and minimum pixel value in the image. This is useful if the image contains e.g. a very bright artifact, which will destroy the dynamic range in the remaining pixels.

Automatic scaling:

nordicICE scales according to the highest and lowest pixel values detected in the image file

Equal scaling for all images:

The same scaling is applied to all images in a series, using the pixel range from the first image loaded.

Default voxel size

The default voxel size in all three orthogonal planes is set here. These values whould reflect the voxel size found in the DICOM/SPM header. If the values are modified, the new values will override the values determined upon image loading. For other image types the values given here will always be used.

SIEMENS Numa 3.x parameter filename identifiers

Siemens Numaris 3.x specific identifier used to recognize mosaic files dependent on the Siemens Parameter filename DICOM tag. This identifier tag is not used in Numaris 4.x. Parameter Filename identifier for Siemens perfusion images: In certain types of MR perfusion images generated under Siemens Numars 3.x, multi-echo images are produced where only one of the echoes represent the actual raw perfusion data. The string specified should be found in the Siemens Parameter filename DICOM tag and is used by nordicICE to identify these types of perfusion series. This identifier tag is not used in Numaris 4.x or for perfusion data generated by any other vendor.

Auto-detect MOSAIC settings:

When checked, converts MOSAIC images without first showing the detected mosaic format. If unchecked, the detected mosaic format can be modified through a dialog box.

DICOM Temp resolution identifier:

Specifies which dicom tag is used to extract the temporal resolution of dynamic image series. If the selected tag is not found or does not contain a valid temporal identifier, an error message will occur during analysis.

Image Formats tab

Related topics: