This page lists the bugs, bug fixes, and minor changes to Jim
version 4.0. Any minor changes should not affect core
functionality of Jim unless otherwise indicated. Fixed versions
of Jim have a minor release indicated by a letter such as
"4.0_j". You can see which version you currently have installed
from the 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 3.0, you need to look at the Jim 3.0 bug parade.
If you want to install the latest release of Jim 4.0, you can either do a full re-install, or you can simply use this link to download the file xinapse.jar. Click right on the link above, and save to a temporary location before using it to replace the file called xinapse.jar in the install directory. If you don't know which is the install directory, do:
find / -name "xinapse.jar" -print
xinapse.jar.
xinapse.jar file before replacing it with the
updated version.
Important Note: if you do a full re-install of the latest version of Jim 4.0, 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.dat file is in the Jim installation directory, then please also ensure that you make a backup copy of license.dat.
Key: type of issue
| Type | Bug/Enhancement Description | Fix Description | Bug ID | Status | Version / date |
|---|---|---|---|---|---|
| b |
Images saved using File->Save As in NIFTI-1 format, do
not have the correct intensity rescale intercept value set. When
viewed in other tools, such as fslview, the intensities values will
be incorrect. Usually the intensities values shown will be 1 greater
than the true value.
|
Fixed. NIFTI-1 images now have the correct value for the "scale intercept" field set when saved. | 40-059 | F | 4.0_p, 07 Apr 2008 |
| b | DICOM images that have unsigned short (16-bit) values that have pixel values greater than 32767 will have incorrect negative pixel values. | Fixed. DICOM images with 16-bit values were converted to signed short images regardless of whether they were signed or unsigned. This worked fine as long as pixel values un unsigned images were less than 32767. Now unsigned short images are converted to PixelDataType.INT to allow the full range of pixel values up to 65535. | 40-057 | F | 4.0_o, 04 Mar 2008 |
| e | DICOM images that original from Varian NMR machines are not handled correctly due to incorrect values in the Varian DICOM header. Specifically, unsigned byte pixel values should have a pixel representation value of 0x0000. However, the value representation recorded in the DICOM header is 0x00FF (255 decimal). | Work-around checks for the origins of the DICOM image, and if the manufacturer is "Varian", then the a value representation of 255 is interpreted as unsigned. Please report any other problems with import/conversion of Varian images. | - | - | 4.0_n, 02 Dec 2007 |
| b | "Select All" menu item in ROI Toolkit's Edit menu is not correctly enabled according to the number of ROIs in the selected image slice. | Fixed. | 40-056 | F | 4.0_n, 02 Dec 2007 |
| b | Smoothing an Irregular ROI with only 3 points can cause the thread that does the smoothing to enter infinite loop, and then Jim consumes lots of CPU. | Fixed. | 40-055 | F | 4.0_n, 02 Dec 2007 |
| B | In MS Lesion Finder tool, registration to template images was not properly implemented when "Reverse Slices" option was selected. Poor registration to template resulted in incorrect lesion volumes being found in MS Lesion Finder. | Fixed. | 40-054 | F | 4.0_n, 02 Dec 2007 |
| b | Images in diffusion-weighted dataset from a Siemens Avanto scanner do not have slice separation set correctly. "pixelZSize" is zero in UNC images. | Fixed. For datasets with multiple image weightings, slice separation is now set from the slice thickness in the image header. | 40-053 | F | 4.0_m, 02 Sep 2007 |
| b | When multiple images (for example, in the Image Concatenator) or files (for example, in the Raw Data Converter) are selected in a list, pressing the "Remove Selected" button may result in the removal of the wrong images/files from the list. | Fixed. | 40-052 | F | 4.0_m, 02 Sep 2007 |
| b | UNC Images sometimes failed to return the image orientation and position information due to incorrect parsing of these values from the image header. | Fixed. | 40-051 | F | 4.0_m, 02 Sep 2007 |
| b | When option "Snap to centre rather than corner of pixels" is set in ROI Toolkit preferences, moving an Irregular ROI Vertex Handle causes the handle to move wildly out of the field of view of the image. | Fixed. | 40-050 | F | 4.0_m, 02 Sep 2007 |
| e | Image Converter now handles Varian images. | - | - | - | 4.0_l, 13 Jun 2007 |
| B | MS Lesion Finder tool outlines the MS lesions in a very unsatisfactory way with some input images. | Fixed. Uniformity correction wasn't performing correctly for some input images with unusual orientations. There were mainly Analyze 7.5 or NIFTI images with the image pixels stored in an unusual orientation. Results using images with more usual orientations should be unaffected by this bug-fix. | 40-049 | F | 4.0_l, 13 Jun 2007 |
| b | In Fuzzy Connector tool and MS Lesion Finder tool, removing an input image from the set of input images could cause error messages suggesting the the number of input images was greater than the number of intensity relations. | Fixed. Removing an input image now clears the cache of input images. | 40-048 | F | 4.0_l, 13 Jun 2007 |
| b | In Fuzzy Connector tool and MS Lesion Finder tool, editing an input image name, but not committing the change by pressing the carriage return key did not cause the input image to be changed. | Fixed. Editing the image name now causes the input image to be changed and the input image cache to be cleared. | 40-047 | F | 4.0_l, 13 Jun 2007 |
| b | NIFTIImages cannot be read correctly from InputStream. | Fixed. Error was incorrect skipping over voxOffset field for InputStream-based reading. | 40-046 | F | 4.0_l, 13 Jun 2007 |
| b | PDF report produced by the BPF calculation in BrainFinder includes a picture of the "CSF-only" image which is inaccurate. The CSF image contains "holes" where the CSF intensity is low. | Fixed. Error was in applying an unsuitable threshold when converting the CSF image to binary (black or white) pixel intensities. | 40-045 | F | 4.0_l, 13 Jun 2007 |
| b | Changing the colour mapping in the Image Overlay dialog does not give the overlaid image the correct contrast settings according to the contrast sliders. | Fixed. Overlay image now has correct contrast when colour mapping is changed. | 40-044 | F | 4.0_l, 13 Jun 2007 |
| b | Attempting to use a "Preset" in the Algebra or Fitter tools, with a formula that contains a ',' character results in the error message: Error saving preset: illegal character ',' in formula. The preset is not saved. | ',' is a legal character, and this error message has now been removed. | 40-043 | F | 4.0_l, 13 Jun 2007 |
| b | Calculation of BPF in BrainFinder tool causes error message "Cannot save CSF image" when working with an image directly loaded from the Image Converter or Raw Converter tools. BPF values cannot be calculated as a result. | This is a regression caused by the fix to Bug ID 40-040. BrainFinder tool should now save images either in the same format as the input image, or in the case of images loaded directly from the Image Converter, in the user's preferred image format set using the Preferences dialog. | 40-042 | F | 4.0_k, 6 Feb 2007 |
| b | A user has reported that Jim can become unresponsive if the user quickly pages through slices during ROI-creation interactions. We have been unable to reproduce this issue, but have identified a potential problem with the code. | Paging though slices during ROI interactions is now not permitted. Please report any continuing problems of Jim becoming unresponsive or if it appears "hung". | 40-041 | F | 4.0_j, 1 Feb 2007 |
| b | Brain finder CSF and Brain images were always saved in the user's preferred image format (set in the user preferences) regardless of the format of the input image. | CSF and Brain images are now saved in the same format as the input image. | 40-040 | F | 4.0_j, 1 Feb 2007 |
| e | DCE-MRI results reports for ROI analysis now contain the patient name, patient ID and scan date (if available from the input image(s)). | - | - | - | 4.0_j, 1 Feb 2007 |
| b | The ROI Toolkit edit menu is not setup properly after a "cut" operation. Items which should be greyed out aren't. | Fixed. | 40-039 | F | 4.0_j, 1 Feb 2007 |
| b | The MultiSliceImage.getInstance() leaves java.io.RandomAccessFiles in an open state when testing whether a particular file is an instance of a NIFTI-1 image. If lots of files are accessed with this method, then eventually this leads to the java.io.IOException "too many open files". | Files are now properly closed after failing the test to see whether they are NIFTI-1 images. | 40-038 | F | 4.0_j, 1 Feb 2007 |
| b | When an UNC Colorpacked (R,G,B) image is used as an overlay image, the transparency setting of the overlay has no effect: the overlay image is always rendered as completely transparent. | Fixed. | 40-037 | F | 4.0_j, 1 Feb 2007 |
| e | MS Lesion Finder tool now has another adjustable parameter for greater flexibility. | The new parameter is the "weight" given to the prior probabilities used in the fuzzy connections algorithm. See updated documentation for more details. | - | - | 4.0_i, 22 Nov 2006 |
| e | DCE-MRI results reports for ROI analysis now contain the (area-under-the-curve) AUC values at times 60s, 120s, 180s and 240s after contrast arrival in the tissue. The tissue AUC values are provided, plus the tissue/plasma AUC values. | This modification makes it easier to extract these commonly-used values from the report. | - | - | 4.0_i, 22 Nov 2006 |
| b | Incorrect saving of UNC COLORPACKED (R,G,B) images to Analyze or Nifti-1 RGB_BY_PLANE format. Pixels are mangled. | Fixed. | 40-036 | F | 4.0_i, 22 Nov 2006 |
| b | When background colour for graphs is set to a non-white colour in the user's preferences, then PDF reports show graphs drawn with a rectangle in the top left corner of the graph in the background colour. | Fixed. | 40-035 | F | 4.0_i, 22 Nov 2006 |
| b | PDF reports for Brain Finder/BPF show images of CSF and brain tissue that are squashed or stretched when analysing images with non-square pixels. | Fixed. | 40-034 | F | 4.0_i, 22 Nov 2006 |
| e | Irregular and CurvedLine ROIs have been made rotatable. | Hold the shift key down and drag any of the corner or edge handles to rotate the ROI. | - | - | 4.0_h, 4 Oct 2006 |
| b | Inappropriate error message given by Query/Retrieve when an image retrieve fails due a bad DICOM image being encountered with corrupt pixel data. | Fixed. | 40-033 | F | 4.0_h, 4 Oct 2006 |
| b | Retrieve of some DICOM series with Query/Retrieve tool may fail with stack trace showing NullPointerException. | Fixed. | 40-032 | F | 4.0_h, 4 Oct 2006 |
| b | Defining an ROI for the arterial input function for the Perfusion and DCE-MRI tools, on a slice that is outside the range of the number of physical slice locations in the input image set, results in an error message that does not give an indication of the source of the error. | Fixed. Error message made more specific. | 40-031 | F | 4.0_h, 4 Oct 2006 |
| b | Pushing the "Save Settings" button in the DCE-MRI tool with "FLASH" selected results in an error message Error: invalid flip angle; preferences not saved. | Fixed. Bad checking of valid flip angle. | 40-030 | F | 4.0_g, 1 Sep 2006 |
| b | In Perfusion and DCE-MRI tools, if image displayed in Jim has different pixel sizes from the images that is being analysed in the Perfusion/DCE-MRI tools, and the Roaming Response dialog is being used, then changing the ROI used to show the response causes the ROI change behaviour to be strange (ROI stretched to the wrong shape or disappear from the display). | Fixed. Cached on-screen shape was being altered according to the pixel sizes in the analysed image, not the on-screen image. | 40-029 | F | 4.0_g, 1 Sep 2006 |
| b | Image Converter failed to import image when DICOM images from the same DICOM Study were anonymised with different anonymised patient names. | Fixed. | 40-028 | F | 4.0_g, 1 Sep 2006 |
| b | It was possible to enter invalid path/file names when creating image file in Jim. | Fixed. The file name is checked for validity every time a new image (and other files) is created. | 40-027 | F | 4.0_g, 1 Sep 2006 |
| b | Display of slice number, mouse location, and pixel intensity under mouse not updated when keyboard accelerators used to zoom, scroll or change displayed slice(s). | Fixed. | 40-026 | F | 4.0_g, 1 Sep 2006 |
| b | Errors in scripts StorageServer, StorageServerTool, QueryRetrieve, RawConverter and RawConverterTool in the Unix directory meant that the scripts would not run. | Fixed. Scripts referred to classes in Version 3.0 that were moved to a different location in Version 4.0. | 40-025 | F | 4.0_g, 1 Sep 2006 |
| b | Using Eraser can result in ROIs that have no area and that are invisible when viewed in Jim. | Fixed. | 40-024 | F | 4.0_g, 1 Sep 2006 |
| b | When saving images in NIFTI-1 format with double-precision pixel values, from Jim's "Save As" menu, message was given than clipping of pixel values was necessary, and saving failed. | Fixed. | 40-023 | F | 4.0_f, 11 Aug 2006 |
| b | In images with unusual numbers of pixels, linking of image slice zoom and scroll sometimes failed. | Fixed. Truncation, rather than rounding of scrollbar settings caused Jim to calculate that slices were not scroll linked. | 40-022 | F | 4.0_f, 11 Aug 2006 |
| b | Vertex position not visible when dragging vertices when editing the outline of a Curved Line or Irregular ROI. Makes editing the outline difficult. | Fixed. Moving vertex drawn in XOR mode during mouse drag. | 40-021 | F | 4.0_f, 11 Aug 2006 |
| b | Raw Data Converter may fail when attempting to convert R,G,B images. Java stack trace shown. | Fixed. R,G,B images may now be converted to colour or greyscale images. | 40-020 | F | 4.0_f, 11 Aug 2006 |
| e | Image Converter (and Image Converter Tool) now allow images to be anonymised. | When anonymisation option is selected, all references to patient name are removed from the output images. Use flag -a for text-mode tool and check the "Anonymise" checkbox for the GUI tool. | - | - | 4.0_f, 11 Aug 2006 |
| b | "Go to Slice" dialog does not function when a new image is loaded into Jim's display. | Fixed. Dialog is now re-enabled when a new image is loaded. | 40-019 | F | 4.0_e, 1 Aug 2006 |
| b | When "Use Brain Finder" option was used in Perfusion Tool, in slices where there was no brain tissue, no masking of the non-brain signal was being performed. | If there is no brain in a particular slice, all pixels in that slice are now zeroed. | 40-018 | F | 4.0_e, 1 Aug 2006 |
| b | Image intensities may flicker when adjusting image contrast/brightness settings, when an image with floating-point or a double pixel values is displayed. Only happens with images that have extremes of brightness values. | Fixed. | 40-017 | F | 4.0_e, 1 Aug 2006 |
| b | Various problems with Slice Extractor, Image Interleaver and Image Concatenator when handling images with more than 3 dimensions. | Fixed. | 40-016 | F | 4.0_e, 1 Aug 2006 |
| b | Image conversion fails for UNC and NIFTI-1 images when image has 4 dimensions. Error message says "invalid info element (2) for dimension 4". | Fixed. | 40-015 | F | 4.0_e, 1 Aug 2006 |
| e | Brain Finder BPF calculation now includes a variable threshold setting to allow fine tuning of the location of the threshold between the CSF and brain peaks in the intensity histogram. The default setting (0.5) leads to behaviour that is the same as in previous releases. A lower setting gives higher BPF values by classifying more signal as brain, while a higher setting gives lower BPF values by classifying more signal as CSF. | - | - | - | 4.0_d, 23 Jun 2006 |
| e | Image Converter now handles Bruker ParaVision™ images. See Chapter 4, Section 2 for more details. | - | - | - | 4.0_d, 23 Jun 2006 |
| b | Default ROI size for Rectangular and Elliptical ROIs was unsuitable for images with small pixels (e.g. < 0.5 mm). | Default ROI size is now dependent on the image pixel sizes. | 40-014 | F | 4.0_d, 23 Jun 2006 |
| B |
Contouring failed in images with unusually small pixel sizes.
Message shown: "contouring failed (dead end)".
This bug also affected the creation of ROIs in the Fuzzy Connector and MS Lesion Finder tools when the image pixel size was significantly less than 1 mm. |
Error in code that formed closed contours - failed to close ROI when pixel size was significantly less than 1 mm. | 40-013 | F | 4.0_d, 23 Jun 2006 |
| B | Expressions with unbalanced parentheses not reported as errors in tools that use expression (e.g. Image Algebra, Image Fitter etc.) | Check for unbalanced is now explicitly made and reported. | 40-012 | F | 4.0_d, 23 Jun 2006 |
| b | Roaming fitting dialog does not show the fitted curve in the Image Fitter tool. Java stack trace may be shown. | Fixed. | 40-011 | F | 4.0_c, 12 Jun 2006 |
| b | Cancelling image registration in Perfusion and DCE-MRI tools did not cause the whole of the analysis task to me cancelled. | Cancelling registration now causes the whole analysis task to be aborted. | 40-010 | F | 4.0_c, 12 Jun 2006 |
| b | Pixel snap had no effect when moving/stretching ROIs. | Centre ROI handles now snap to the centre of pixels when pixel snap turned on. Other ROI handles snap to the corners of pixels. | 40-009 | F | 4.0_c, 12 Jun 2006 |
| b | Preferred image type not always saved in Jim's user preferences. | Program did not save the user's preferred image class, just the last class to be listed in the Preferences dialog. | 40-008 | F | 4.0_c, 12 Jun 2006 |
| B | Poor registration of images in Perfusion and DCE-MRI toolkit. | Image registration in these toolkits is now constrained to in-plane translation and rotation, resulting in more reliable and faster registration. | 40-007 | F | 4.0_c, 12 Jun 2006 |
| b | Exporting animated GIF images from JMovie does not take account of the "Step between frames" setting. | Fixed. | 40-006 | F | 4.0_c, 12 Jun 2006 |
| b |
Selecting "Save As ..." from the File menu of JMovie results in a
NullPointerException, when the movie image is created
from an image already loaded into Jim.
|
Not all data structures were copied from Jim's main display when creating the movie image. | 40-005 | F | 4.0_c, 12 Jun 2006 |
| b | Jim freezes when loading very large UNC images. | Fixed. | 40-004 | F | 4.0_c, 12 Jun 2006 |
| e | Contrast arrival time and analysis end time are now shown on the Roaming Response graphs in the Perfusion and DCE-MRI toolkits. | - | - | - | 4.0_b, 17 May 2006 |
| e | User can now set an "analysis end time" to truncate data to be analysed in the Perfusion and DCE-MRI toolkits. | Data after the "analysis end time" is ignored. | - | - | 4.0_b, 17 May 2006 |
| b | When more than one slave display present, pane layout of only first slave display changed when master display layout changed. | Fixed. | 40-003 | F | 4.0_b, 17 May 2006 |
| b | NIFTI image header extensions not handled correctly. Extensions not added to images as expected, and image loading failing when attempting to read extensions. | Fixed. | 40-002 | F | 4.0_b, 17 May 2006 |
| B | AIF lead/lag feature does not function correctly. This bug affects both the DCE-MRI and the Perfusion toolkits. The time-shift of the data for the tissue response relative to the AIF does not happen. That shift in time was happening for both the tissue response and the AIF and either the AIF or the tissue response were being corrupted (depending on whether you set a lead or a lag). Results where a zero lead/lag was entered are unaffected by this bug. | Code has been reworked to provide the correct shift in time between the AIF and the tissue response when a lead/lag is non-zero. User documentation has been updated to make it clear that the "time of contrast arrival" is the time at which the signal changes (due to contrast agent) either in the tissue or in the vessel where the AIF is measured (whichever comes first). | 40-001 | F | 4.0_b, 17 May 2006 |
| - | New release. | - | - | - | 4.0_a, 01 May 2006 |