Bugs and Fixes in Jim Version 7.0

This page lists the bugs, bug fixes, and minor changes to Jim version 7.0. 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 "7.0_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.

If you're looking for the latest bugs and fixes for Version 6.0, you need to look at the Jim 6.0 bug parade. If you're looking for the latest bugs and fixes for Version 5.0, you need to look at the Jim 5.0 bug parade. If you're looking for the latest bugs and fixes for Version 4.0, you need to look at the Jim 4.0 bug parade.

If you want to install the latest release of Jim 7.0, you can either do a full re-install, or you can simply use this link to download the file xinapse7.jar. Click right on the link above, and save to a temporary location before using it to replace the file called xinapse7.jar in the install directory. If you don't know which is the install directory, do:

Note: Please be sure and rename the current xinapse7.jar file before replacing it with the updated version.

Important Note: if you do a full re-install of the latest version of Jim 7.0, 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

Also added the ability to anonymise the patient accession number to the Anonymiser.
Type Bug/Enhancement Description Fix Description Bug ID Status Version / date
b Conversion of diffusion-weighted Bruker ParaVision images fails with a stack trace that shows java.lang.ArrayIndexOutOfBoundsException. Fixed. 70-100 - 7.0_47, 02 Jul 2021
b Dongle licensing fails with SafeNet dongles under Windows after Windows Update. Fixed. 70-099 - 7.0_46, 16 Jun 2021
b Java stack trace shown in DCE-MRI analysis when creating report, and a Predefined AIF is used where the AIF time-course is shorter than the image data. Fixed. 70-098 - 7.0_45, 15 Mar 2021
b LicenseServer software failed to serve licenses for mixed versions of Jim. Fixed. 70-097 - 7.0_44, 19 Mar 2019
b Parsing of XML InfoExtendedData in NIFTI images failed if there were extra null characters after valid XML text. Fixed. 70-096 - 7.0_43, 15 Feb 2018
b Bruker image conversion fails to set slice thickness and image positions correctly when both the "method" and "visu_pars" files are missing. Conversion now falls back to using the "acqp" file if present. 70-095 - 7.0_42, 10 Jan 2018
e Fast Save File Lists have been enhanced to allow the specification not of only of the Fast Save file name, but also the image format in which to save (NIFTI-1, Analyze, UNC or DICOM). - 70-094 - 7.0_41, 04 Jan 2018
b Error message "cannot calculate histogram bin size for pixels of infinite intensity" may be shown when displaying single-precision Complex images with vary large pixel intensities. Fixed. 70-093 - 7.0_41, 06 Dec 2017
b When using Image Converter and saving to disk, if different output iamge formats (such as Analyze, NIFTI and UNC) are selected in succession, the Image Converter may report that the image already exists on disk, even though the image is in a different format. Fixed. 70-092 - 7.0_40, 06 Nov 2017
b Node-locked licensing may not work on newer versions of Linux where the "ifconfig" command is no longer present. Fixed. 70-091 - 7.0_40, 06 Nov 2017
b Image slices from GE scanners may be sorted into the wrong anatomical order when using the Image Converter. Ordering should always be increasing slice number from foot->head, right-left and anterior->posterior. Fixed. 70-090 - 7.0_39, 19 Oct 2017
b When trying to start Jim, Java stack trace with java.lang.StringIndexOutOfBoundsException shown when running under Java 9. Fixed. 70-089 - 7.0_38, 03 Oct 2017
e New stand-alone text-mode program to make an atlas from an image and a set of annotated ROIs. This program is called Roi2Atlas. The ROI annotations are sorted and are used to convert the image to a set of integer-labelled VOIs. A table of ROI annotations and their integer labels is printed on standard output. - 70-088 - 7.0_37, 12 Jul 2017
b Jim 3D shows an error message "3D graphic environment is not installed". Fixed. Caused when the startup folder set in the user preferences no longer exists (for example when it was set in a removable drive, and the drive was removed). 70-087 F 7.0_37, 12 Jul 2017
e Enhancement to allow the Anonymiser to store anonymised DICOM files in a particular folder, rather than in the folder "Anonymised" which is a sub-folder of the original DICOM images. - 70-086 - 7.0_36, 20 Jun 2017
b When saving ROI files, the file chooser allows the selection of an Image/J ROI file filter, implying that the ROIs will be saved in the correct file format for Image/J. Fixed. Jim cannot save ROIs in Image/J ROI file format; the file filter has been removed when saving an ROI file. 70-085 F 7.0_36, 20 Jun 2017
b Screen shot in 3-D display caused Jim to hang. Fixed. Later versions of Jim used the latest version of Java3D, which does not allow drawing into off-screen buffers for screen capture. Method of screen capture has been changed, but be aware that any windows placed in from of the 3D display will be captured as part of the screen shot. 70-084 F 7.0_35, 19 May 2017
B For patients who were entered into General Electric scanners in a feet-first position, the image slices were in the wrong order when converted. Fixed. Please report any further problems with ordering of slices. 70-083 F 7.0_34, 04 May 2017
B Slices in diffusion-weighted images were not being sorted into the correct order by the Image Converter. Fixed. Please report any further problems with ordering of slices. 70-082 F 7.0_34, 04 May 2017
B Incorrect intensity scaling may be applied when converting Bruker ParaVision images. Fixed. Please report any further intensity rescaling issues. 70-081 F 7.0_33, 31 Mar 2017
b Dongle licensing may not work on later versions of OS X. Fixed. Please be sure to install the dongle driver software, and the dongle license.txt file if licensing doesn't work with a dongle. 70-080 F 7.0_32, 20 Mar 2017
e Added new tool "ToRGB" to the "Organise" menu. This tool takes three greyscale input images and produces a colour output image with each of the three input images contributing to of the red, green or blue colour channels. This tool is also available as the stand-alone program "ToRGB" (command-line version) and "ToRGBTool" (GUI version). - 70-079 - 7.0_31, 10 Mar 2017
b Change to installer. Java3D is now installed in the Jim 7 installation folder, rather than into the JRE. This change was made because upgrading Java can result in the deletion of Java3D files, requiring the re-installation of Jim. Please report any problems with installation, or Java3D. 70-078 F 7.0_30, 31 Jan 2017
b Conversion/import of large Bruker images is excessively slow. Improved. Certain values that were being repeatedly calculated from the Bruker header files are now cached, speeding up conversion by a factor of about 8. 70-077 F 7.0_29, 18 Jan 2017
e When diffusion-weighted Bruker images are imported/converted, the diffusion weighting b-factor, gradient vector and b-matrix values are now recorded in the image header. - 70-076 - 7.0_29, 18 Jan 2017
b In ROI Totaliser report, ROI statistics are not reported separately for Colour=0 when ROIs with user-specified colours are present. Fixed. When ROIs with user-specified colours are present, the category of ROI with Colour=0 is reported just like the categories of ROI with other colours. 70-075 F 7.0_29, 18 Jan 2017
b In Brain Follow-Up, brain extraction does not always work. Fixed. Please report any problems with brain extraction in Brain Follow-Up. 70-074 F 7.0_29, 18 Jan 2017
b If keys are remapped in the "Keyboard Accelerators" tab of the preferences window, changes are not remembered after restart of Jim. Fixed. 70-073 F 7.0_28, 16 Nov 2016
b Java stack trace with java.lang.NullPointerException may be shown when a key is pressed and no image is loaded. Fixed. 70-072 F 7.0_28, 16 Nov 2016
b Conflict between options to set Patient ID and Study ID in program DicomSend - both used. option --id. Fixed. Patient ID is now set using option --pid. 70-071 F 7.0_27, 24 Oct 2016
b Error may be shown when converting or retrieving DICOM images stored at 8 bits/pixel with short data type. Fixed. 70-070 F 7.0_27, 24 Oct 2016
b Database manager did not correctly delete patients from the database. Subsequent Query/Retrieves to the database resulted in a list of patients including those that were deleted from the database, but those patients had no image series when queried. Fixed. 70-069 F 7.0_26, 18 Oct 2016
b When importing an image series from the DICOM Query/Retrieve which has mixed numbers of image rows/columns/slices, a NullPointerException may be shown. Fixed. 70-068 F 7.0_26, 18 Oct 2016
b In Jim's 3-D viewer, when loading/viewing ROIs and viewing them as an iso-surface, a java stack trace with NullPointerException may be shown if ROIs fill or extend beyond the image field-of-view. Fixed. 70-067 F 7.0_25, 31 Aug 2016
e In ROI Propagation toolkit, the R-R interval or the time between image frames can now be read from the input image in the VFR and PWV analyses. A checkbox has been added for the user to try to get them from the image. If they cannot be gotten, an error message is shown. - 70-066 - 7.0_24, 04 Aug 2016
b "Save Settings" in ROI Propagation toolkit does not save all settings. Fixed. 70-065 F 7.0_24, 04 Aug 2016
b DCE-MRI analysis does not work with DICOM input images. NullPointerException thrown. Fixed. 70-064 F 7.0_24, 04 Aug 2016
b Noisy input data in DCEMRI tool can give rise to infinite values for ve in Tofts models, which results in an inability to display the ve image. Fixed. Infinite and NaN values are now trapped. 70-063 F 7.0_23, 15 Jun 2016
b In Perfusion and DCEMRI analysis toolkits, the contrast arrival time and analysis end time are not correctly set from the user preferences after clicking on the "Save Settings" button. Fixed. 70-062 F 7.0_23, 15 Jun 2016
b Java stack trace with NullPointerException shown when performing DCEMRI analysis with a reference image and the "Register time-series" option selected. Fixed. 70-061 F 7.0_23, 15 Jun 2016
b Java stack trace shown when using image Converter in text mode, when converting image such as as screen captures, where the pixel size is undefined, resulting in a zero pixel size. Only seen when creating NIFTI-1 format images. Fixed. 70-060 F 7.0_22, 14 Jun 2016
B Wrong slice ordering when importing/converting sagittal DICOM-4 images. Jim should order slices with increasing left coordinate with slice number, but this was not always the case, and depended on the order in which slices were stored within the DICOM image.

Global slice position and orientation incorrectly set when importing/converting image with mixed orientations (such as seen in localiser images).

Fixed. 70-059 F 7.0_22, 14 Jun 2016
e Better integration of Jim with Mac OS X. New installer using IzPack. - 70-058 F 7.0_22, 11 Jun 2016
b Jim does not work properly on Mac OS X running OS X 10.9, 10.10 or 10.11. Symptoms include very slow and poor quality graphics, and unexpected stack traces showing that methods and classes cannot be found. Fixed. The fixed requires a move away from the Apple-supplied Java 1.6.0 to the Oracle-supplied Java 1.7 or 1.8. Thus, Java must be installed from the Oracle web site, and the a complete re-installation of Jim is needed. Please see Chapter 2 of the Manual, Section 6. (Apple Macintosh installation). 70-057 F 7.0_21, 20 May 2016
b "Sort by median" radio button was not hidden when extended statistics were not shown. Fixed. 70-056 F 7.0_21, 20 May 2016
b Image Converter does not set slice order or slice orientation correctly with some Bruker ParaVision images. Fixed. 70-055 F 7.0_20, 18 Apr 2016
b Java stack trace shown with NullPointerException thrown when loading NIFTI images with UNKNOWN extended header data. Fixed. 70-054 F 7.0_19, 07 Apr 2016
e Enhancement to allow font sizes to be scaled to screen size as a user preference. - 70-053 F 7.0_18, 03 Apr 2016
b Philips DICOMDIR files with enhanced DICOM images not correctly parsed, leading to images not being found within the DICOMDIR. Fixed. 70-052 F 7.0_18, 03 Apr 2016
b Working directory (folder) is not changed in ImageSelectionPanels (such as those used in the Image Least-Squares Fitter) if the folder/file text is edited by hand, or the folder/file text is copied and pasted into the text field. Fixed. 70-051 F 7.0_17, 19 Feb 2016
b JPEG images missing from Manual folder in Jim installation folder. Fixed, but will require a re-install of Jim to get the missing JPEG images. - F 7.0_17, 19 Feb 2016
b Dongle licensing with Safenet dongles no longer works for Mac OS X 10.11 (El Capitan) and later. Fixed. Please report any further problems with dongle licensing. 70-050 F 7.0_17, 19 Feb 2016
b When saving images that have a non-standard slice order using Jim's "Save As" function in NIFTI-1 format, and FSL compatibility mode is selected in the user preferences, the slice order may be reversed. Fixed. Please report any further problems with slice reversing when an image is saved. 70-049 F 7.0_16, 24 Dec 2015
b Stack trace shown with java.lang.ArrayIndexOutOfBoundsExceptionwhen Image Stats dialog is shown, and minimum intensity contrast slider is set to the same intensity as the maximum intensity constrast slider and when working with floating-point images. Fixed. 70-048 F 7.0_16, 24 Dec 2015
e Added a new ROI propagation calculation module for dedicated volume flow rate (VFR) calculation from phase contrast angiography images. Previously, VFR calculation was possible using the PVW calculator, but this module makes the calculation more streamlined. - 70-047 F 7.0_16, 24 Dec 2015
b Image information is not saved when using "Save As ..." from Jim's File menu. Fixed. 70-046 F 7.0_15, 18 Nov 2015
b Image Converter is very slow when converting large multi-frame DICOM images. Improved. String representation of DICOM elements is now cached. 70-045 F 7.0_15, 18 Nov 2015
b Image intensity scaling is wrong when converting multi-frame Philips images where each image slice (frame) is independently scaled. Fixed. 70-044 F 7.0_15, 18 Nov 2015
b Jim will not start when using a Microcosm dongle on Mac OS X 10.11 (El Capitan). Fixed. 70-043 F 7.0_14, 24 Oct 2015
e New options added to the Roivol stand-alone program.
  • -s,--slice Separate ROI statistics by image slice number.
  • -w,--write-stats Write individual ROI statistics in the same format as the "Write Statistics" function in Jim.
- 70-042 - 7.0_14, 24 Oct 2015
b Behaviours of GUI version and command-line version of Image Resampler are different when reorienting images. The orientation of the output image may be different. The behaviour of the "reversed slice order" setting has been rationalised and made consistent for the GUI and command-line versions. In particular:
  • The anatomical order of the slices is read from the image if that information is present, and the user has not set the image orientation manually.
  • If the user has not set the image orientation manually, and the anatomical order of the slices is not present in the image, the slice order is assumed to be anatomically correct.
  • If the user has set the image orientation manually, then the slice order is assumed to be anatomically correct, unless the user specifies reversed order using the checkbox in the GUI tool or the -r option in the command-line version.
Fixed. 70-041 F 7.0_14, 24 Oct 2015
b Rounding error when writing quaternion values to NIFTI image header can given erroneous orientation when using images produced by Jim in SPM. Fixed. 70-040 F 7.0_13, 15 Oct 2015
b When loading a movie image into JMovie using the "Load Movie from Stack" function, if an error occurs when loading the image stack, then a pop-up error message dialog is shown, but a Java stack trace is also shown. Fixed. Just the pop-up error message dialog is shown now. 70-039 F 7.0_13, 15 Oct 2015
b Cannot specify rotation angle for Image Resampler on command line with option --rotate: null pointer exception thrown. Fixed. 70-038 F 7.0_13, 15 Oct 2015
b Problem with License Server not serving licenses on systems running OpenJDK. Fixed. 70-037 F 7.0_12, 14 Sep 2015
b DICOM Anonymiser did not create disk files with correct File Meta information. Fixed. 70-036 F 7.0_12, 14 Sep 2015
b Saving an image in DICOM format results in a disk file that, in many circumstances, ended with ".dcm", regardless of whether this was specified by the user. This wa contrary to the DICOM standards, and has been removed. Fixed. 70-035 F 7.0_12, 14 Sep 2015
b Dongle licensing does not work on Mac OS X systems when using Safenet dongle. Fixed. 70-034 F 7.0_11, 31 Aug 2015
b Java stack trace shown with NullPointerException thrown when registering NIFTI images in two-file format. Fixed. 70-033 F 7.0_11, 31 Aug 2015
b When running Jim under Java 1.8, the Multi-Planar Reconstruction dialog shows a corrupt 3-plane view of the reconstructed volume. Fixed. Caused by bug in Java 1.8. 70-032 F 7.0_11, 31 Aug 2015
b When loading DICOM images with no slice position information, Java Stack Trace may be shown, with NullPointerException thrown. Fixed. 70-031 F 7.0_10, 7 Aug 2015
b When working with imported images that have been dragged-n-dropped from the Image Converter, the message may appear: "Error: com.xinapse.importimage.ImportedImage is does not implement com.xinapse.image.WritableImage." Fixed. 70-030 F 7.0_10, 7 Aug 2015
b Java stack trace may be shown with java.lang.NullPointerException if imported images are dragged-n-dropped onto tools such as the Algebra Tool, and the 'Apply' button is clicked multiple times. Fixed. 70-029 F 7.0_10, 7 Aug 2015
B Slice ordering incorrect for DICOM4 images from Philips MRI scanner. Fixed. Please report any further problems with slice ordering. 70-028 F 7.0_10, 7 Aug 2015
b When saving ROIs, if the 'Append' option is selected and the ROIs are saved multiple times, the number of deleted ROIs in the ROI file can build up exponentially. Fixed. 70-027 F 7.0_10, 7 Aug 2015
b Java stack trace may be shown in Error Console when loading a new movie image and Movie Profile dialog is visible. Fixed. 70-026 F 7.0_10, 7 Aug 2015
b Cannot perform DICOM Query/Retrieve from a McKesson PACS (Medcon) server. Server reports that Element (0x0000,0x0700) [Priority] is missing. Fixed. Please report any further problems with PACS connectivity. 70-025 F 7.0_9, 25 Jun 2015
b Java stack trace will be shown if more than one ROI is selected in different slices, and a joint histogram is displayed, but image slices have different contrast settings. Fixed. 70-024 F 7.0_9, 25 Jun 2015
b In Least-Squares Fitter, when performing roaming fit and dragging the mouse over the image to show the fitted curve at different locations, Jim can hang. Fixed. Caused by having repeatedly re-opening a file and not closing the file, giving too many open files. 70-023 F 7.0_9, 25 Jun 2015
b In Least-Squares Fitter, functions that are self-initialising (require no initial guesses for the fit variables) may still require the user to provide initial guesses for some input images. Fixed. Linearisation of the fitted function to generate the initial guesses was failing for some unusual input data. 70-022 F 7.0_9, 25 Jun 2015
b LicenseServer cannot be automatically started on Microsoft Windows systems using the Windows Task Manager. Fixed. Please see the new instructions for installing the License Server, noting that the task to be started is now LicenseServer.exe, not LicenseServer.bat. 70-021 F 7.0_8, 05 Jun 2015
b Image contrast range cannot be expanded when Orthogonal View dialog is open. Fixed. 70-021 F 7.0_7, 22 May 2015
e Added a DICOM private Sequence element to indicate that anonymisation has taken place. The Sequence contains three Elements:
  • <0x0caf, 0x1063> VR=Code String VM=1 Xinapse Systems Anonymisation Flag
  • <0x0caf, 0x1065> VR=Date VM=1 Xinapse Systems Anonymisation Date
  • <0x0caf, 0x1067> VR=Time VM=1 Xinapse Systems Anonymisation Time
- 70-020 - 7.0_7, 22 May 2015
b When entering contour intensity contour level in ROI toolkit dialog, the value cannot be specified to more than one decimal place. Fixed. Can now enter up to 4 decimal places. 70-019 F 7.0_7, 22 May 2015
b When paging through the slices of an image while zoomed in, the image can slowly drift to the right and downwards as the image scroll amount changes. Fixed. 70-018 F 7.0_7, 22 May 2015
b Image intensity rescale slope and intercept values were incorrectly propagating through to output images from input images in the following tools:
  • Image Algebra
  • Image Fitter
  • Image Registration
Fixed. 70-017 F 7.0_7, 22 May 2015
b ROI intensity-related statistics not written when using "Write statistics" from the ROI Toolkit's "File" menu. Fixed. 70-016 F 7.0_6, 27 Mar 2015
e Work-around for DICOM images that contain incorrectly encoded element <0x0010, 0x0032> Patient Birth Time with VR of "DA" (should be "TM"). Caused stack trace when anonymising images, and when converting them. Fixed. 70-015 F 7.0_6, 27 Mar 2015
b Option --version or -ver did not print out the version message for the SliceExtractor program. Fixed. 70-014 F 7.0_6, 27 Mar 2015
e Added new keyboard accelerator (default key: 'z') so that ROIs can be finalized not just by double-clicking, but also by pressing a key on the keyboard. The types of ROI that can be finalized in this way are:
  • Irregular and Curved Line ROIs.
  • Open and Closed Spline ROIs.
  • Contoured ROIs - the key-press substitutes for a single click on the mouse to finalize the contour.
- 70-013 - 7.0_5, 13 Mar 2015
B In Image Resampler, when working with Analyze 7.5 images, and user preferences were set to only save images in a non-flipped orientation, then the resulting resampled image could have images inadvertently flipped. This bug also caused Analyze 7.5 images shown as iso-surfaces in the 3-D display to become reversed in orientation when the surface fidelity was set to high or extra-high. Fixed. 70-012 F 7.0_5, 13 Mar 2015
b In 3-D display, iso-surface generation failed when image contains NaN (not-a-number) pixel intensity values. Fixed. NaN values are now treated as zero intensity for the purposes of iso-surface generation. 70-011 F 7.0_5, 13 Mar 2015
b Dongle licensing did not work on 64-bit Linux systems. Fixed. 70-010 F 7.0_4, 02 Feb 2015
b Java stack trace may be shown when using Jim's 3-D viewer with an image directly imported by drag-and-drop onto an Iso-Surface selector, and the surface fidelity is altered: java.lang.InternalError: com.xinapse.importimage.ImportedImage
at com.xinapse.importimage.ImportedImage.getCopy(ImportedImage.java:2084)
...
Fixed. 70-009 F 7.0_4, 02 Feb 2015
b In image algebra tool, masking of the output image did not work when using the Image Masking options. Fixed. 70-008 F 7.0_4, 02 Feb 2015
b Java stack trace may be shown when working with floating-point images, and displaying Image Stats Dialog with normalised Histogram, and the maximum intensity slider value is below that of the minimum intensity slider, e.g. java.lang.ArrayIndexOutOfBoundsException: -22
...
Fixed. 70-007 F 7.0_3, 09 Jan 2015
e Update to import of Bruker images produced using ParaVision 6. Handling of image intensity rescaling updated; handling of date formats updated; handling of new characters in text fields updated. - 70-006 - 7.0_3, 09 Jan 2015
b Java stack trace is shown when working with an image that has been directly imported from the Image Converter or Query/Retrieve, and the ROI totaliser is used: java.lang.NullPointerException
at java.io.File.(File.java:277)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
...
Fixed. 70-005 F 7.0_3, 09 Jan 2015
b When loading images into the Image Overlay, using the 'Previous Images' menu, or when using an Image File Chooser, Jim can hang. Fixed. Update to bug ID 70-001: deadlock could occur when loading an image. 70-004 F 7.0_3, 09 Jan 2015
B Fuzzy Connector and MS Lesion Finder may fail to identify all fuzzy-connected regions. On some images, there are regions that clearly should be identified, and are identified in the slices above and below, but which are not outlined by ROIs. Fixed. If you find any unexpected 'missing' ROIs on certain slices, where ROIs are seen on the slices above and below, then please report this. 70-003 F 7.0_2, 11 Dec 2014
b On Mac OS X, Jim did not co-exist fully with MatLab due incompatibility of Java 3D versions. Fixed. Jim has been modified so that it can run with older versions of Java 3D, supplied as part of the standard Apple Java 1.6 distribution. Jim does not now need the installation of later versions of Java 3D. However, some functionality is lost if the old version of Java 3D is retained: zooming in using the mouse scroll-wheel does not work with the 3-D display in Jim. 70-002 F 7.0_2, 11 Dec 2014
b When dragging and dropping an image file onto the Image Overlay dialog, the overlay image file name was not shown in the ImageSelectionPanel. Fixed 70-001 F 7.0_2, 11 Dec 2014
- New release. - - - 7.0_1, 09 Nov 2014
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