Bugs and Fixes in Jim Version 9

This page lists the bugs, bug fixes, and minor changes to Jim version 9. Any minor changes should not affect core functionality of Jim unless otherwise indicated. Fixed versions of Jim have a minor release indicated by a number after the underscore "_", such as "9_1". You can see which version you currently have installed by selecting About from the Help menu. Comparison with the table below will indicate whether a bug you have noted needs to be reported, or has already been fixed.

For bugs and fixes for previous versions, see:

If you want to install the latest release of Jim 9, you can either do a full re-install, or you can simply use this link to download the file xinapse9.jar. Click right on the link above, and save to a temporary location before using it to replace the file called xinapse9.jar in the install directory. If you don't know which is the install directory, do:

Note: Please be sure to rename the current xinapse9.jar file before replacing it with the updated version.

Important Note: if you do a full re-install of the latest version of Jim 9, and have performed any customisation of the installation (such as editing the Unix shell script Jim), then please be sure and make backup copies of these changed files in another directory before installing Jim again. If your license.txt file is in the Jim installation directory, then please also ensure that you make a backup copy of license.txt.

Key: type of issue

Key: status of bugs

Type Bug/Enhancement Description Fix Description Bug ID Status Version / date
e Enhancement to Cardiac Segmental Intensities. New option to allow zero-intensity pixels to be ignored when calculating the mean and the standard deviation of segment intensities. - - - 9_21, 07 Sep 2024
e Enhancement to Cardiac Segmental Intensities. In addition to the mean segment intensities, the standard deviation of segment intensities is written to reports. - - - 9_20, 19 Aug 2024
e Various enhancements to DTI Tractography to make it more suitable for images with small pixel sizes, and to improve performance.
  • Tract smoothing filter width has finer adjustment and smaller minimum value.
  • Tract rendering displays tracts with fidelity that adapts to the image pixel size.
  • When rendering tracts as tubes, tube diameter has finer-grained settings, and minimum tube size is smaller.
  • When saving tracts to disk, point spacing has finer-grained settings, and minimum spacing between points is smaller.
  • Improved speed when removing or replacing displayed tracts.
 - - 9_19, 16 Aug 2024
e Added a new option to Cardial Segmental Analysis, Segment Intensities to allow zero-intensity pixels to be ignored when calculating mean and standard deviation of segment intentensities. - - - 9_20, 07 Sep 2024
b DTI Tractography may hang while tracking on images with small pixel sizes. Fixed. 9-033 Fixed 9_19, 16 Aug 2024
e Added a new Preset to the Image Fitter tool, for T1/R1 estimation from Modified Look-Locker (MOLLI) MRI pulse sequence. - - - 9_18, 24 Jul 2024
b Scan TR, TI and echo train length could not be read from DICOM images. - 9-032 Fixed 9_18, 24 Jul 2024
b Cord Follow-Up fails on MacOS systems with Error: could not refine cord: support vector machine cord.svm not found". Can also affect CordFinder if option to refine the centre-line is selected. Fixed. jar file missing from CLASSPATH on MacOS. - - 9_17, 01 May 2024
e Enhancement to Cord Follow-Up, to allow both forward registration and reverse registration directions to be visualised. The half-way images for both directions are written, together with their corresponding ROIs. The new option for the command-line version is -b,--both, and there is a new check-box in the GUI version.

When this option is selected, the output images and ROI file names are prefixed by hwFwd for the forward direction, and hwRev for the reverse direction.

- - - 9_17, 01 May 2024
b DICOM images from older GE scanners with Big-Endian encoding could not be converted to other formats (e.g. NIFTI). - 9-031 Fixed 9_16, 15 Apr 2024
b Images with double-precision pixel intensity values could not be saved in DICOM format. Fixed. 9-030 Fixed 9_16, 15 Apr 2024
b Bug in Cord Finder tool when run from command-line meant that:
  • VRML file was always written, whether requested or not.
  • Text report was never written to terminal.
- 9-029 Fixed 9_15, 04 Apr 2024
e Enhancement to Cord Follow-Up tool, to allow cord centre-line refinement to NOT be performed. Default is still to perform centre-line refinement.

Also, fixed bug in error messaging which meant that failures when run from GUI were not being reported.

- - - 9_15, 04 Apr 2024
b Further issues with Bruker ParaVision 360 images. Stack trace may be shown when importing/converting images. Fixed. 9-028 F 9_15, 04 Apr 2024
e More flexible floating licensing. A single floating license will now allow one Jim program and one stand-alone tools program to run simultaneously. - - - 9_14, 25 Mar 2024
b Bruker ParaVision may appear rotated, depending on the subject positioning in the MRI machine. Fixed. 9-027 F 9_14, 25 Mar 2024
b Stack trace with NumberFormatException shown when importing/converting Bruker ParaVision 360 images with run-length encoded (RLE) arrays in auxiliary files. Fixed. 9-026 F 9_13, 18 Mar 2024
E Changes to Cord Follow-Up tool:
  • Defaults to doing a fine spline-based slice-wise final registration of the straightened cord images at the two time-points. New option to turn off this new feature, reverting to the previous behaviour (option -n,--no-spline-reg).
  • Can save the cord co-registration transforms to an XML file so that they can be applied to a different pair of images with the same geometry. (option -w,--write to write the transforms, and option -r,--read to read and apply the transforms).
- - F 9_12, 29 Feb 2024
b Loading very large images with floating-point, complex or long pixel intensity values can cause Jim to hang. Fixed. Caused by an int overflow. 9-025 F 9_11, 26 Feb 2024
b License Server for floating license may show stack trace, something like:

X11 connection rejected because of wrong authentication.
Exception in thread "Thread-1" java.awt.AWTError: Can't connect to X11 window server using 'localhost:0.0' as the value of the DISPLAY variable.

Fixed. 9-024 F 9_11, 26 Feb 2024
b For floating (network) license, license client may fail to obtain a floating license from the License Server due to a SSL connection failure. Fixed. SSL connection have been made more secure in some later versions of Java 17. Security has been updated to enable these more secure connections. The fix will need the new xinapse9.jar file to be installed on both the client and server computers. 9-023 F 9_11, 26 Feb 2024
b In Image Converter, may see java.lang.NullPointerException when converting multi-frame DICOM MR images where the flip angle is not defined in the DICOM header. Fixed. 9-022 F 9_11, 26 Feb 2024
b In Image Fitter, Roaming Response, when fitting with ADC, the graph does not show the fitted exponential decay curve. Fixed. 9-021 F 9_11, 26 Feb 2024
B When an image has:
  • some slices with all zero intensity pixels before slices with non-zero intensity pixels, and
  • image pixel intensity values are small floating-point values.
then the Image Statistics dialog shows an incorrect zero mean intensity for the whole image (i.e., when there is no slice selected). 		Fixed. 9-020 F 9_10, 01 Dec 2023
B Various errors relating to the creation of files and folder on Windows platform. These errors are caused by trying to set POSIX file permissions on a non-POSIX-compliant operating system such as Microsoft Windows.

Error messages including the phrase 'posix:permissions' not supported as initial attribute may be shown.

Fixed. Please report any further problems. 9-019 F 9_10, 01 Dec 2023
B When performing affine image registration using a saved transform (.rtp file), and the "Invert the pre-calculated transform" check-box is selected, and there are multiple images to register, then the transform is only applied successfully to every other image in the image in the list of images to register. The remaining images have the forward transform applied. Fixed. 9-018 F 9_9, 18 Apr 2023
b In CordFinder, the option to set the order of longitudinal variation of the cord shape to zero, was missing. Modified to allow a zero setting for "order of longitudinal variation", which then results in a cord shape that does not vary between slices.
N.B. the command line option to this has now changed to -o,--order, to reflect the fact that the number of B-splines is not set explicitly by this option. 		Fixed 9-017 - 9_8, 30 Mar 2023
b In CordFinder, writing cord shape to VRML file resulted in a corrupted cord surface, with the first and final surface quadrilaterals having spurious 'spikes'. Fixed 9-017 - 9_8, 30 Mar 2023
b Saving images with floating-point pixel values in DICOM format may generate an Exception stating that floating-point values may not be put to the image. Fixed 9-016 - 9_7, 02 Mar 2023
e Added ability to write ROI coordinates in LPS, RAS or xyz coordinate space to ROI Toolkit. - 9-015 - 9_7, 02 Mar 2023
b Error and stack trace with "/ by zero" is shown on performing some multi-threaded operations on systems with very large number of processors. Fixed. 9-014 F 9_7, 02 Mar 2023
B In pixel-by-pixel Perfusion/DCE-MRI analysis, when invalid results are obtained for a particular pixel, zeros were always written to the output parameter maps, regardless of the setting for write zeros/NaN values is the user preferences. Fixed. 9-013 F 9_6, 07 Feb 2023
b Deadlock may occur when viewing slave display frames, with frames unable to refresh. Fixed. 9-012 F 9_6, 07 Feb 2023
b Stack trace with java.lang.ArrayIndexOutOfBoundsException make be shown when viewing Hollow ROIs in orthogonal views. Fixed. 9-011 F 9_6, 07 Feb 2023
B Incorrect scaling of phase images affecting images mainly from Philips scanners. Phase values may have been doubled. Fixed. 9-010 F 9_6, 07 Feb 2023
b In VFR and PWV calculations, when creating a report, the x-axis label of graphs incorporated into reports was incorrectly labelled with units of "ms" (milliseconds) rather than "s" (seconds). Fixed. 9-010 F 9_6, 07 Feb 2023
b When loading an image in the main display, when there linked displays, the linked displays do not have their zoom and scroll reset to match that of the main image. Fixed. 9-009 F 9_5, 13 Oct 2022
B In Image Statistics dialog, when "Show normalised" checkbox is selected, the image statistics Histogram is not updated correctly when the contrast/brightness intensity sliders are adjusted. Furthermore, when the "Show normalised" checkbox is de-selected, the histogram shown is still normalised. Fixed. 9-008 F 9_5, 13 Oct 2022
e In BrainAtrophy tool, registration of templates images (GM, WM and CSF priors etc) to T1-weighted image may fail in various circumstances:
  • Images that have been de-faced or masked.
  • Images that have relatively poor resolution or non-uniformity.
  • Images that unusual contrast.
 Various improvements have been made to try to overcome these issues, and two new options provided to help:
  • Affine registration of the template image to the T1-weighted image can now optionally use mutual information as the cost function. This is useful when the image contrast is unusual.
  • Extra regularisation can be introduced for the diffeomorphic registration of the template image to the T1-weighted image. This is useful when local instabilities in the registered template images is seen.
9-007 - 9_5, 13 Oct 2022
E In the BrainAtrophy tool, if lesion ROIs are present on the original (unregistered) FLAIR image, these are transformed to the registered FLAIR image space, and may be used for lesion segmentation. - 9-006 - 9_5, 13 Oct 2022
b Java stack trace with java.lang.IndexOutOfBoundsException may be shown when writing very large images. Fixed. Jim can now handle images with up to 231-1 (2147483647) pixel primitive values. 9-005 F 9_5, 13 Oct 2022
B In Image Statistics dialog, when no slice was selected, Histogram and mean intensity shown related to the first slice visible on screen, rather than to the whole of the slices shown on screen. Fixed. 9-004 F 9_5, 18 Aug 2022
b Could not find HostID on some Mac OSX systems. Fixed. 9-003 F 9_4, 22 Jun 2022
b When stand-alone Header program was invoked with too many arguments, error message was output, but program did not exit. Fixed. 9-002 F 9_3, 13 Jun 2022
e New chemical exchange saturation transfer (CEST) processing module added. - - - 9_3, 13 Jun 2022
e New stand-alone text-only program RoiTotals added. This produces ROI and VOI statistics in the same format as are output from the ROI Toolkit's 'Calc' → 'Totals'. - - - 9_2, 03 Feb 2022
b Main display does not have keyboard focus when an image is loaded, so keyboard accelerators do not work unless the mouse is clicked on the main display. Fixed. 9-001 F 9_1, 05 Jan 2022
- New release. - - - 9_0, 08 Dec 2021
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