DICOM or image data

Stradview is capable of loading most DICOM data directly, so long as it is either RAW, JPEG, lossless JPEG2000 or some subsets of RLE. The data can either be stored as a single frame per DICOM file, or as a single multi-frame DICOM file.

In order to load DICOM data, select 'All files' from the 'File->Open' dialog, and then open any file within the DICOM sequence. Stradview will automatically find all files in this numerical sequence, and regard the file with the lowest numerical value as frame zero. Alternatively, a DICOM series can be selected using 'File->Open directory'. Once loaded, DICOM data is stored internally in a similar format to that saved in the DICOM files. If this is not an 8-bit format (for example CT data is stored as 16-bits), this is converted to an 8-bit format for display according to the current windowing parameters.

To change these windowing parameters, use the 'rotate' tool and click and drag in the review (top left) canvas. Dragging up and down changes the window width (i.e. the range of CT values to display) and dragging left and right changes the window centre (i.e. the CT value to map to mid-grey). Windowing of the current frame is updated dynamically as you drag the mouse. Once you have finished dragging, the current windowing parameters are then applied to all the other display windows. Alternatively, windowing can be changed with the DICOM display dialog.

DICOM data can be visualised and segmented in the same way as normal Stradview data. However, if you want to keep any additional information you have created from the data (for instance window parameters, or a set of segmented contours) you will need to save the data as a Stradwin file. Stradwin DICOM files only consist of an additional text '.sw' file - the actual DICOM data is never overwritten. The '.sw' file merely contains all the additional Stradwin data and a reference to the original DICOM data files.

Once you have saved a DICOM data set as a Stradwin file, loading the '.sw' file next time will load the DICOM data and all the associated Stradview parameters. You can work on this data set just as if it were a conventional Stradwin file - for instance, if you want to export only every other frame to a new file, you can use 'File->Export frames' as usual. This operation only affects which frames are loaded by Stradview, and in which order - it does not affect the original data. 'File->Export frames' can also be used to create a sequence of images from the DICOM data.

Image sequences

Stradview can also load images stored in either TIFF, JPEG, PNG or BMP formats. Any file names in these formats which contain a sequence number will be interpreted as a contiguous sequence of frames. Stradview can also load multi-frame TIFF files. Just select 'All files' from the 'File->Open' dialog and click on one of the image files in the sequence.

Of these formats, TIFF is the only one which can store 16-bit data and is hence often used for micro-CT data sets. If the TIFF data is 16-bit, then the windowing functions will be used to determine how to display this data as an 8-bit image. These function can also be used to convert the raw data values to other, more manageable, units. Stradview also understands a very specific TIFF format which is output by wxDicom when applying Refined Metal Artefact Reduction (RMAR) to CT data containing metal. This format also contains the 3D location of each image as well as the image scale and windowing settings.

Image sequences are interpreted in the same way as DICOM data: the files are never overwritten, but instead a new '.sw' file is created which contains links to the original image files. The '.sw' file also contains any additional data (for instance manual positions or object contours) created by Stradview.

Other formats

Stradview can also interpret some part of the Mindways '.qct' format, the ITK '.mhd' format, Analyze '.hdr' or '.img' format, and nearly raw raster data '.nrrd' format, in a similar way to DICOM data and image sequences.

Opening directories

It is also possible to open all the files contained in a given directory. This is particularly useful if the DICOM or image files do not have an obvious sequence number (for instance if the file names have been randomised by an anonymiser). To do this, select 'Open directory' from the selection criteria box, then select any file in that directory.

In this case, files will be initially opened in alphabetical order. If they are DICOM files, the sequence order can then be corrected later once the slice positions have been read in. The default file name for the corresponding new Stradview file will be in the higher level directory so that the actual directory contents are not disturbed.