This page lists the bugs, bug fixes, and minor changes to Jim version 8.0. 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 "8.0_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.
For bugs and fixes for previous versions, see:
If you want to install the latest release of Jim 8.0, you can either do a full re-install, or you can simply use this link to download the file xinapse8.jar. Click right on the link above, and save to a temporary location before using it to replace the file called xinapse8.jar in the install directory. If you don't know which is the install directory, do:
Note: Please be sure and rename the current xinapse8.jar file before replacing it with the updated version.
Important Note: if you do a full re-install of the latest version of Jim 8.0, 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
| Type | Bug/Enhancement Description | Fix Description | Bug ID | Status | Version / date |
|---|---|---|---|---|---|
| b | DICOM images from older GE scanners with Big-Endian encoding could not be converted to other formats (e.g. NIFTI). | Fixed. | 80-057 | F | 8.0_24, 15 Apr 2024 |
| 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. | 80-056 | F | 8.0_23, 17 Apr 2023 |
| b | Error and stack trace with "/ by zero" is shown on performing multi-threaded operations on systems with very large number of processors. | Fixed. | 80-055 | F | 8.0_22, 23 Feb 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, the 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. | 80-056 | F | 8.0_23, 17 Apr 2023 |
| B | When using Image Converter with Philips DICOM images, intensity rescaling may not be correctly applied. | Fixed. | 80-054 | F | 8.0_21, 06 Dec 2021 |
| B | When using Image Converter, image slices make in non-standard (reverse) order when converting DICOM images with all image slices in a single DICOM file. | Fixed. | 80-053 | F | 8.0_20, 28 Nov 2021 |
| b |
In DTI Analysis tool, two issues:
|
Fixed. | 80-052 | F | 8.0_19, 19 Nov 2021 |
| b | In Brain Atrophy tool, when working with NIFTI-1 format images, during "Stage 2", the registered and prior images may not be found when using a mixture of compressed and uncompressed images. | Fixed. | 80-051 | F | 8.0_19, 19 Nov 2021 |
| b | In Brain Atrophy tool, lesion marker ROIs in original FLAIR image are not transformed to registered FLAIR image space. | Fixed. | 80-050 | F | 8.0_19, 19 Nov 2021 |
| b | Conversion of multi-frame Bruker ParaVision images (e.g. a contrast-enhanced dynamic series) may fail to convert all image time-points. | Fixed. | 80-049 | F | 8.0_19, 19 Nov 2021 |
| b |
Conversion of diffusion-weighted Bruker ParaVision images fails with a
stack trace that shows java.lang.ArrayIndexOutOfBoundsException.
|
Fixed. | 80-048 | F | 8.0_18, 02 Jul 2021 |
| b | In Picture Converter, java stack trace shown if FoV is set by user, rather than pixel sizes. | Fixed. | 80-047 | F | 8.0_17, 18 Jun 2021 |
| b |
When performing analysis in various tools where the input image has
been dragged-and-dropped from the Image Converter tool, java stack
trace may be show similar to:
java.lang.ClassCastException: com.xinapse.i.r cannot be cast to com.xinapse.multisliceimage.Analyze.ANZImage |
Fixed. | 80-046 | F | 8.0_17, 18 Jun 2021 |
| b | Dongle licensing can fail with SafeNet dongles under Windows after Windows Update. | Fixed. | 80-045 | F | 8.0_17, 18 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. | 80-044 | F | 8.0_16, 20 Apr 2021 |
| b | Fuzzy Connector / MS lesion finder asked user if they wanted to create a report, even if the operation was cancelled. MS Lesion Finder caused Java stack trace to be shown when creating a report, or cancelling a report. | Fixed. | 80-043 | F | 8.0_15, 19 Mar 2021 |
| b | Particle analysis, when performed with 3-D connections, can fail to identify all particles. | Fixed. | 80-042 | F | 8.0_15, 19 Mar 2021 |
| b | Image Resampler caused image corruption when resampling Analyze/NIFTI colour images. | Fixed. | 80-041 | F | 8.0_15, 19 Mar 2021 |
| b | Some tools within Jim (BrainAtrophy, Cardiac Segmental Analysis, Cord Finder, Fuzzy Connector, Perfusion and DCE-MRI) may hang on Mac OS X due to a GUI-related deadlock when using OS X native (Aqua) Look & Feel. | Fixed. Please report any futher problems with Jim hanging under OS X. | 80-040 | F | 8.0_14, 21 Jul 2020 |
| b | File choosers for Registration Transform Parameter (.rtp) files used in Image Registration did not filter correctly. .rtp files could only be selected by selecting "All Files" in the file filter. | Fixed. | 80-039 | F | 8.0_14, 16 Jul 2020 |
| b | Incorrect Preset formula for 4-point Diffusivity Measurement in Image Algebra tool, gives error message 'formula contains an unknown variable "T2^3"'. | Fixed. | 80-038 | F | 8.0_13, 19 Jun 2020 |
| b | Image Converter. Conversion of Bruker images with multiple echoes recorded in the "acqp" file may fail, if the image data does not really contain multiple echoes. | Fixed. | 80-037 | F | 8.0_13, 19 Jun 2020 |
| b | In Cardiac Analysis, insertion point handle was drawn in wrong position in some circumstances. | Fixed. | 80-036 | F | 8.0_13, 19 Jun 2020 |
| b |
When diffeomorphically registering 2-D images, images with a zero slice thickness will
cause the error "divergence detected; try increasing regularisation".
Effectiveness of diffeomorphic registration is compromised for images with small pixel sizes. |
Fixed. | 80-035 | F | 8.0_13, 19 Jun 2020 |
| B | In ROI Toolkit, when propagating contour ROIs in 3-D, ROIs were not created in all slices within the specified range. | Fixed. | 80-034 | F | 8.0_13, 19 Jun 2020 |
| B | In Image Resampler, image rotation causes image corruption for images that have unequal numbers of pixel rows and columns. | Fixed. | 80-033 | F | 8.0_13, 19 Jun 2020 |
| B | Image Stats dialog may not show correct intensity histogram for images with non-integer pixel intensities. | Fixed. | 80-032 | F | 8.0_13, 19 Jun 2020 |
| b | LicenseServer software failed to serve licenses for mixed versions of Jim. In addition, when mixed versions of Java are used on the LicenseServer computer and the client computer, license serving can fail with the message "javax.net.ssl.SSLHandshakeException: no cipher suites in common". This is due to changes in SSL security in later version of Java. If this error is encountered, the latest xinapse8.jar file needs to be installed on both the client and the license server. | Fixed. | 80-031 | F | 8.0_13, 19 Jun 2020 |
| e | Enhancement to reorder image slices when converting Bruker ParaVision™ images with multiple echoes. | Image slices are reordered to give:
|
80-030 | F | 8.0_12, 15 Feb 2019 |
| b | Java stack trace may be shown when attempting to read a comma-separated list of floating-point values, if the items in the list are not comma-separated. | Fixed. More meaningful error message is shown, with the hint that this should be a comma-separated list. | 80-029 | F | 8.0_12, 15 Feb 2019 |
| b | Conversion of DICOM images with large/small 'Rescale Slope' or 'Rescale Intercept' could lead to clipping or truncation of pixel intensity values. | Fixed. Conversion of this type of DICOM image now results in an image with floating-point pixel intensity values. | 80-028 | F | 8.0_11, 8 Sep 2018 |
| b | Large DICOM images with floating-point pixel values stored in a private element could not be loaded. | Fixed. | 80-027 | F | 8.0_11, 8 Sep 2018 |
| b | Various tools may leave orphaned ProgressMonitors showing progress through actions and that allow cancellation of the action. These ProgressMonitors remain on-screen even when the action is complete. | Fixed. | 80-026 | F | 8.0_10, 19 Aug 2018 |
| e | Enhancement to Image Masker to allow a 4-D image to be masked using a set of ROIs defined on one 3-D volume from the 4-D set. | 80-025 | F | 8.0_10, 19 Aug 2018 | |
| b | In Cardiac segmental Analysis, radial divider lines were not distinctive enough on HiDPI screens. | Fixed. | 80-024 | F | 8.0_10, 19 Aug 2018 |
| b | Stack trace with java.lang.ArrayIndexOutOfBoundsException may be shown when editing the outline of Hollow ROIs. Deleting vertex on a Hollow ROI may result in additional vertex being deleted. Inserting vertices on a Hollow ROI may result in vertices being inserted in the wrong place. | Fixed. | 80-023 | F | 8.0_9, 26 May 2018 |
| e | Enhancement to give scaling of user-interface elements that is appropriate to the resolution of the display. This enhancement mainly affects users of HiDPI monitors, such as Retina displays on Apple Macintosh, and UHD (4K) monitors. | - | 80-022 | - | 8.0_8, 17 May 2018 |
| b | Diffeomorphic registration may fail with java.lang.IndexOutOfBoundsException on multi-core processors with lots of cores, and small image matrices. | Fixed. | 80-021 | F | 8.0_7, 03 May 2018 |
| b | DICOM Storage Server will not accept connections from other DICOM nodes. | Fixed. | 80-020 | F | 8.0_7, 03 May 2018 |
| b | Pressing the PageUp/PageDown/Home/End/Right/Left/Up/Down in a text field (such as the image contrast min/max values) caused the selected image slice to change. | Fixed. Selected image slice does not change if a text field has the input focus. | 80-019 | F | 8.0_7, 03 May 2018 |
| b | Pop-up Progress Monitor was not shown for Brain Follow-Up tool, and therefore Brain Follow-Up operations could not be cancelled in GUI version of tool. | Fixed. | 80-018 | F | 8.0_7, 01 May 2018 |
| e | Stack trace with java.lang.IndexOutOfBoundsException may be shown when diffeomorphically registering images with large differences between the numbers of image pixel rows and image pixel columns. | F | 80-017 | F | 8.0_6, 16 Apr 2018 |
| e | Enhancement to Cord Finder to allow unfolded cord image to be written with the field-of-view the same as the input image, rather than half the field of view, which is the default. | - | 80-016 | - | 8.0_6, 16 Apr 2018 |
| B | In Cord Finder, when creating an "unfolded" cord image, the field-of-view of the unfolded cord image was shifted by half a pixel in both the A-P and L-R directions, resulting in a slightly offset cord centre line on this image. | Fixed. The cord centre-line is low at coordinate (0,0) in the axial plane. | 80-015 | F | 8.0_6, 16 Apr 2018 |
| b |
In VFR calculation in ROI Propagation tool, check-box added to allow user to specify that
phase correction based on a stationary tissue ROI file is to be done. This is less confusing
than just not selecting an ROI file when correction is not to be done.
In addition, contents of ROI Propagation Tool are now scrollable, since the tool window (with the addition of these new contents) was getting too big for smaller screens. |
Fixed. | 80-014 | F | 8.0_6, 16 Apr 2018 |
| b | In Cord Finder running in GUI mode, unfolded cord images was not written to disk even when check-box to do so was selected. | Fixed. | 80-013 | F | 8.0_6, 16 Apr 2018 |
| e |
Image Converter now allows images with multiple echo times to be output as:
|
- | 80-012 | - | 8.0_5, 05 Apr 2018 |
| b | Java stack trace may be shown when cropping a 4-dimensional image: java.lang.IndexOutOfBoundsException: invalid dimension: 3 | Fixed. | 80-011 | F | 8.0_5, 05 Apr 2018 |
| b | Java stack trace may be shown when using Image Converter and saving b-value and b-matrix tables to disk: java.lang.IndexOutOfBoundsException: bad slice number for b-value at com.xinapse.importimage.ImportedImage.getSliceDWbValue(ImportedImage.java:1202) | Fixed. | 80-010 | F | 8.0_5, 05 Apr 2018 |
| B | In VFR and PWV calculations in ROI Propagation tool, mapping from phase image values to flow velocity was incorrect for General Electric MRI scanners. | Fixed. The mapping requires the use of the magnitude image as well as the phase image, and provision has been made to input the magnitude image. | 80-009 | F | 8.0_5, 05 Apr 2018 |
| e | In VFR calculation in ROI Propagation tool, stationary tissue phase value is now selected using an ROI file, rather than entering a phase image intensity value. Also, mean velocity at each time-point is also reported. | - | 80-008 | - | 8.0_5, 05 Apr 2018 |
| e | In VFR and PWV calculation in ROI Propagation tool, now attempts to get the R-R interval from the image info field "<0x0018, 0x1062> Nominal Interval" before reverting to using "<0x0018, 0x1060> Trigger Time". | - | 80-007 | F | 8.0_5, 05 Apr 2018 |
| b | In Diffeomorphic Registration, when multiple images to register are selected, registration of the first image image is done correctly, but all subsequent images are not registered, but are only deformed using the deformation calculated for the first image. | Fixed. | 80-006 | F | 8.0_4, 28 Mar 2018 |
| b | Dongle licensing doesn't work, because a key DLL is missing from the installer. | Jim 8 must be re-installed to get this fix. | 80-005 | F | 8.0_4, 28 Mar 2018 |
| E |
Major improvements to Brain Atrophy tool.
|
- | 80-004 | - | 8.0_3, 07 Mar 2018 | b |
Image is not displayed correctly under the following circumstances:
|
Fixed. | 80-003 | F | 8.0_3, 07 Mar 2018 |
| e | Modification so that when running on the command-line using a floating (network) license, request for a license will keep retrying until a license is available. Previous behavior was to exit the program if a floating license request was denied. | Fixed. | 80-002 | - | 8.0_3, 07 Mar 2018 |
| b | Licensing was redesigned for Version 8 to allow older versions of Jim to run using a Jim Version 8 license. However, this feature did not work and only Version 8 licenses could be validated from a Version 8 license file. | Fixed. | 80-001 | F | 8.0_2, 15 Feb 2018 |
| - | New release. | - | - | - | 8.0_1, 01 Feb 2018 |