General User Preferences

This brings up the Preferences dialog:

• The Look and Feel. Make Jim look and behave more like a regular (non-Java) application on your computer platform. Select your preferred Look and Feel from the list at the top.
  Note: the available Looks and Feels depends on your type of computer. For example, the Windows Look and Feel is only available on the Microsoft Windows platforms.
  Note: Jim will need to be restarted before this option takes effect.

• The display sizes for the Main display window, for Slave windows, and for the Movie windows. Enter the sizes in screen pixels.
  Note: these are the sizes of the areas in which images are actually displayed.

• The display layout.

• Which slice you want selected when an image is loaded into Jim. Select:
  • None if you want no slice to be selected.
  • First if you want the first image slice to be selected.
  • Middle if you want the middle image slice to be selected.
  • Last if you want the last image slice to be selected.

• Whether you want the master/slave displays to be linked when Jim is first started.

• How you want the mouse scroll wheel to behave when zooming in on the image image using the scroll wheel. You can configure Jim so that a scroll-down action zooms in (the default) or out.
  Note: Jim will need to be restarted before this option takes effect.

• Page size and page orientation for Jim's PDF reports.

• The display units.

• Whether you want interpolation on or off. You can set this separately for the master (main) display and any slave displays.

• The complex display mode.

• The type of image you want selected in file choosers. You can setup Jim so that image file choosers have a filter for UNC images, for Analyze™ or for NIFTI-1 images as the default.

• Whether you want to allow UNC images to be overwritten without asking.

• If you work with Analyze™ images, Jim can read and create compressed (gzip) image files on disk (.hdr.gz and .img.gz). If you would like Jim to create compressed disk files for your Analyze™ images automatically, then select the Compressed button.

• If you work with NIFTI-1 images, Jim can read and create compressed (gzip) image files on disk (.hdr.gz, .img.gz, and .nii.gz). If you would like Jim to create compressed disk files for your NIFTI-1 images automatically, then select the Compressed button.

• If you use images in the a NIFTI-1 format, you can choose whether Jim will create images in one file (with extension .nii) or in the traditional Analyze two-file format (.hdr and .img files).

• The folder (directory) where you want Jim to startup. This is particularly useful if you use Microsoft Windows and keep your images in a particular location. To select a new startup folder either edit the text or click the button and select the folder using the File Chooser that pops up.

• When one of Jim's tools is closed, and the check-box is ticked, any input image names will be cleared from the Image Selection panels, and they will have to be re-selected if the same tool is re-opened. If this preference is not ticked, the input images will be retained in the Image Selection panels when the tool is next re-opened.

• If the check-box is ticked, and a pixel-by-pixel fitting procedure in one of Jim's tools fails, the value "not-a-number" (NaN) will be written to the (floating-point) output image for that pixel location. If not selected, the value zero (0.0f) will be written. Tools that are react to this preference include the Image Fitter, DCE-MRI and Dynamic Analysis tools.

• The number of images to maintain in the Recent Images menu (maximum 30).

• Converter creates images with POSIX-compliant names. Jim's Converter Tool uses information such as the patient's name when creating image file names. These names may contain characters from character sets that are not supported by your operating system, and can cause problems. To prevent this, select this option and the Converter Tool will then translate the names using only POSIX-compliant file names (with a restricted character set).

• Do not warn about negative pixel widths in Analyze 7.5 images. Normally, negative pixel sizes are considered to be illegal by Jim, and it pops up a warning message. However, some programs use negative pixel sizes to indicate than an image should be flipped horizontally before it is displayed. If you select this option, Jim will do the flip automatically whenever an image is opened (by any of the processing tools), and reset the pixel size to a positive value.

• Do not warn about negative pixel heights in Analyze 7.5 images. This causes Jim to behave as above if it encounters a negative pixel height in an Analyze 7.5 image, automatically flipping the image vertically.

• Flip Analyze 7.5 images upside down even if the header says they shouldn't be. Some packages incorrectly set a non-flipped image orientation in Analyze 7.5 images so that when displayed by Jim, the images appear upside down. If your Analyze images appear upside down, and the image header shows a non-flipped orientation, then set this check-box and reload the image.

• Do not flip Analyze 7.5 images the right way up even if the header says they should be . Some packages incorrectly set a flipped image orientation in Analyze 7.5 images so that when displayed by Jim, the images appear upside down. If your Analyze images appear upside down, and the image header shows a flipped orientation, then set this check-box and reload the image.

• Create new Analyze 7.5 images only with non-flipped orientations . Some packages do not correctly display Analyze 7.5 images that have one of the flipped image orientations set in the image header, but display them upside down. By default, Jim creates new Analyze 7.5 images with a flipped orientation. If Analyze images created by Jim appear upside down when viewed using SPM, MRIcro or Image/J, then set this check-box. Any Analyze 7.5 images created by Jim will then have a non-flipped orientation and should be displayed correctly by these packages.

• FSL-compatibility mode for NIFTI-1 images with no orientation information. If the fsl package encounters a NIFTI-1 image with no orientation information (neither qform nor sform) set in the header, the orientation defaults to axial with an increasing patient left coordinate with increasing stored pixel data column number. This is at variance with the standard NIFTI 'c' library. Selecting this option in the preferences will instruct Jim to use the same default orientation as fsl.
  Also, when writing NIFTI-1 images where the orientation cannot be determined, Jim writes default qform nor sform transforms that set the image orientation to axial, with an increasing patient left coordinate with increasing stored pixel data column number.

• Save NIFTI-1 images in an SPM-compatible orientation, when possible. SPM and fsl display packages do not correctly display NIFTI-1 images that are not in one of their 'preferred' orientations. Images may be displayed upside-down or left-right reversed. Selecting this check-box should ensure that when new images are created by reorienting images with the Image Resampler or Multi-Planar Reconstruction, they will be created with a pixel ordering that is suitable for display in SPM and fsl. Images saved in NIFTI-1 format using Save As or ToNIFTI will also be saved in a compatible orientation.

To go to the default setting press the button. To undo any changes you have made to your settings, press the button, but don't forget to press the button if you previously saved them.

Click the button when you have finished setting your preferences.