Importing and Converting Images

Importing and Converting means changing a bunch of importable image files (such as DICOM files) into one of the multi-slice image formats (Analyze, NIFTI-1, NIFTI-2, UNC or multi-slice DICOM). The importing/converting process involves organising the images so that the resulting images each represent one "scan". What's the difference between importing and converting?

Jim can import/convert images in the following medical image file formats:

If you have images in a format not currently supported, please contact Contact Xinapse Systems support to discuss your requirements.

To import/convert images in one of these formats, select Image Converter ... from the File menu. Image file converter.

The Image Converter window will now appear:

The Medical Image Converter tool

The Converter allows you to build a DICOM-like Patient/Study/Series/Acquisition/Image Tree structure, from images contained in a directory or set of directories. You can then select a particular group of related images and load them as a 3-dimensional image data set.

Selecting the Images to be Converted

First, select the images files (such as DICOM files) to be converted. Click the Select files button button to choose the image files. You select either a directory containing some files, or individual files within a directory (press the SHIFT or CONTROL keys on your keyboard to select multiple directories or files). To convert Bruker ParaVisionTM images, select the directory (or directories) that contain the entire image data set(s). To convert Varian/Agilent images, select either individual FDF files, or folder(s) containing FDF files.

You can add more files to the list by clicking the Button to add files to convert button. Then, press the Scan for images button button.

Alternatively, if you are reading your DICOM images from an offline image source, such as a CD-ROM, there may be a DICOMDIR file on the disk. A DICOMDIR file lists all the scans that are present on the CD-ROM, and scanning the DICOMDIR file is much quicker than reading all the image headers. Click the Scan dicomdir for images button button to use this method of scanning for images. A File Chooser will pop up, allowing you to select the DICOMDIR file on the CD-ROM. The image scan will then begin.

After scanning through the files you have chosen, the Converter will build a "tree" structure of patients and scans. Double click on one of the patients listed to show the individual image series (scans) for that patient, as shown below for patient "V.C".

The Medical Image Converter tool showing a
                                  tree of images

Double clicking on any part of the list either expands of collapses that part of the list.

Importing or Converting

To import images (load into the Jim's viewer), select "Load result". To batch convert images, select "Save to disk".

Selecting whether to load and image or save
                                  it to disk

If you do not want to import or convert all slices of a particular scan, then double click on the series node for that scan to expand it and show the nodes for the individual image slices. If a series has multiple acquisitions, then double click on the acquisition node also. Use the SHIFT and CONTROL keys on your keyboard as you click on the slices you want (to select more than one slice). In the example below, the CONTROL key was pressed as the mouse was clicked on the individual slices, to select just slices 1, 3, 5 and 6 of Series 4.

Convert individual slices

Press the SHIFT key as you click to select a complete range of slices.

Anonymising the Converted Images

If you want to anonymise the patient details, select the Check box to anonymise the images as they are converted check-box before you start the conversion or import. The patient name and other patient details (such as the patient's maiden name, address and 'phone number) will be stripped from the images as they are created. If the input images are DICOM images, all private DICOM elements will be removed on conversion. In addition, the file name of the image created will not contain the patient's name.

Note: You can anonymise DICOM files without converting them using the DICOM anonymiser tool.

Configuring Image Converter

The following options are available under the Configure menu:

Menu to configure the Image Converter tool

Click the Button to finish with the Image Converter tool button in the Image Converter when you have finished with importing or converting images.

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