General User Preferences

You can customise how Jim appears and behaves when it first starts up, to match your own preferences. Select Preferences ... from the Toolkits menu:

This brings up the Preferences dialog:

There are five tabbed panes: click on the tab at the top to select the preferences you want to change.

Appearance & GUI

Using this, you can select the following settings for Jim when it initially starts:

• 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.
• Font size. If you find Jim's fonts too small to read comfortably, you can increase the font sizes by selecting either "Medium" or "Large" fonts.
  Note: Jim will need to be restarted before this takes effect.
• Scale GUI components to screen resolution. On high-resolution screens (with lots of pixels), the fonts may be too small to read, and buttons too small to click easily. When this option is selected, user-interface components are increased in size in proportion to the number of pixels in the vertical direction. On screens with 1080 pixels in the vertical direction, standard-sized fonts and components are used; on screens with more than 1080 pixels in the vertical direction, fonts and components are enlarged; on screens with fewer than 1080 pixels in the vertical direction, fonts and components are reduced in size.
  Note: Jim will need to be restarted before this 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.

• How you want the master/slave displays to be linked when Jim is first started. You can choose:

  • Unlinked.
  • Linked. The slave displays are updated by changes made to the Master display.
  • Linked bi-directionally. The slave displays are updated by changes made to the Master, and vice versa.

• Whether you want the Image Preview to be enabled when you are selecting an image using the Image File Chooser. Note: enabling Image Preview uses a lot of computer power and can slow down the selection of an image, especially if your images are compressed.

• 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.

Miscellaneous Settings

Click on the Misc tab to bring up:

Using this, you can select the following settings for Jim when it initially starts:

• The display units.
• Whether you want interpolation on or off. You can set this separately for the master (main) display and any slave displays. If interpolation is turned on, what sort of interpolation to use when displaying the images on-screen.
• 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, Analyze^TM images, NIFTI-1 or NIFTI-2 images or DICOM images as the default.
• Whether you want to allow UNC images to be overwritten without asking.
• If you work with Analyze^TM 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^TM images automatically, then select the Compressed button.
• If you work with NIFTI 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 images automatically, then select the Compressed button.
• If you use images in the a NIFTI 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 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 selected, the GPU will be used for some image registration tasks, in the Quasi-Auto Cord Finder, and for segmenting WM lesions in the Brain Atrophy tool.
• 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 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).
• When writing tables and graph data to text files, how you want the columns of data to be delineated. You can have a space (" "), Tab or (comma (",") character between columns.

Interoperability

Click on the Interoperability tab to bring up:

Here, you can restrict the file names that can Jim can create automatically, and set how Jim behaves when handling Analyze^TM and NIFTI images that have been processed using other packages, or are to be processed further by other packages.

• 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 images with no orientation information. If the fsl package encounters a NIFTI 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 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 images in an SPM-compatible orientation, when possible. SPM and fsl display packages do not correctly display NIFTI 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 format using Save As, ToNIFTI1 or ToNIFTI2 will also be saved in a compatible orientation.

• ROI position output coordinate system. When outputting ROI positions in 3-D space from within the ROI Toolkit, you can choose the coordinate system for the ROI positions:

  • L,P,S. First coordinate increases to the subject's left; second coordinate increases to the subject's posterior; third coordinate increases to the subject's superior. This is the coordinate system used by DICOM. Coordinate units are mm.

  • R,A,S. First coordinate increases to the subject's right; second coordinate increases to the subject's anterior; third coordinate increases to the subject's superior. This is the coordinate system used by SPM, FSL etc. Coordinate units are mm.

  • x,y,z. First coordinate increases with image column number (to the right as viewed on screen); second coordinate increases with image row number (to the bottom as viewed on screen); third coordinate increases with increasing slice number. Coordinate units are mm.

DICOM Settings

Click on the DICOM Setting tab to bring up:

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Here, you can configure how Jim's DICOM features behave.

• When you save an image in DICOM format and the imaging Modality, Patient Position or Pulse Sequence type (for MR images) cannot be determined, you can set values that will always be used, or you can get Jim to ask the user. Select the automatic values from the drop-down menus, or select to have Jim to always ask the user.
• When using Jim's Query/Retrieve tool, you may find that the remote DICOM node you are trying to retrieve images from does not support C-GET operations as a service-class provider (SCP). By default, Jim tries to use a C-GET operation to retrieve images. However, you can configure Jim to use C-MOVE instead. C-MOVE is a more complicated operation since it needs to have a separate DICOM Storage Server set up to receive the images. To use C-MOVE in Query/Retrieve:
• Select "Use C-MOVE, not C-GET in Query/Retrieve operations".
• Jim will then, by default, use an internally-configured Storage Server. In this case, set the port number and AE Title to be used for the internal Storage Server. These details will be needed to set up the remote DICOM node that you are querying.
• If you select "Use an external Storage Server for C-MOVE operations when saving to disk", then the retrieved images will be sent to an external DICOM node for storage. In this case, set the name, I/P address, port number and AE Title that are used by the external Storage Server. The I/P address, port number and AE Title will be needed to set up the remote DICOM node that you are querying.
  Note: images will only be sent to this external Storage Server when you select in the Query/Retrieve tool.
  Note: you can use Jim's own Storage Server to receive the images, either on the computer you are using, or on a remote computer.

Keyboard Accelerators

Jim's keyboard accelerators can be reconfigured here. Each action in the left-hand column has a default key-press, as shown in the second column. If you want to use a different key instead for a particular action, select the Checkbox in the 'Remap' column, and then click on the cell to right of the checkbox. Next, type a new key into that cell, to use the new key as the accelerator for that action.

If you receive a message that the key is already in use, then you can either choose a different key for the action, or you can first remap the action for the key that is in use.

Note: some of these accelerators are case-insensitive, and you will be unable to use neither the upper-case nor the lower-case key as an accelerator if it is in use. For example, the 'i' accelerator to initiate creation of an Irregular ROI can be typed as either a lower-case 'i' or an an upper-case 'I'. You will not be able use either 'i' or 'I' as a remapped key unless you first remap the accelerator to create an Irregular ROI.

For each tab, after you have set your preferences, press the button to save your changes permanently. These settings will then be used next time you start Jim.

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.