**************** LIFEx public version 5.10 *****************
version 5.10 - Fri Jui 14 11am CEST 2019
What's new in (feature release) LIFEx 5.10?
- fixed (texture protocol): add a permanent message when file path of xls result file is wrong in a script file
- fixed (texture protocol): z rezampling (on 2D images) is set to 1 when z spacing value is less than current z spacing
- fixed (texture protocol): declare up to 4000 styles in a .xls workbook
- fixed (texture protocol): null results on all GLCM maps
- fixed cal_min and cal_max values on saved nifti file
- fixed IPP location on 4D nifti file format
- fixed nifti filename includes seriesDescription and title field
- fixed accuracy of values less than 10e-6 on ROI with main interface vs texture accuracy values
- fixed: some axial slices skipped on display when using wheel mouse navigation
- fixed: slices navigation using keyboard
- fixed: operation add,sub on series
- fixed: on some Siemens PET Dicom files, "Actual Frame Duration" dicom field empty can produce a wrong SUV conversion
- added: MIP processing with video card (largely increased performance)
- added: save in 4D nifti format
- added: multiple series management using scripts (see texture UserGuide for more information)
- added: substract, add,.. between times series is available
- added: LIFEx.Image.ImageOrientationPatient=true/false properties in properties file
- added: LIFEx.Image.ImagePositionPatient=true/false properties in properties file
- added (Dsc-MR protocol): add rCBF value in legend of ROI curve
- added (Dsc-MR protocol): add rCBF, rCBV, MTT, TTAB, and parameters of gamma function in ROI value display (and csv, xls)
- improved (texture protocol): increase in performance of CONV_peak calculation (4 times faster)
- improved (texture protocol): loading of all ROIs in directory when it is set on script line
- improved: loading PMOD format of ROI (voi)
**************** LIFEx public version 4.90 *****************
version 4.90 - Thue Apr 9 15pm CEST 2019
What's new in (feature release) LIFEx 4.90?
- added: header viewer of nifti format image
- added: ROI interpolation between two 2D ROI drawn on axial slices
- added: (texture protocol): quartile Q1, Q2 (median), Q3 in conventional indices
- added: loading 2D ROI in PNG, TIFF, BMP, GIF, JPG formats
- added: saving 3D image in nifti integer 16 bit signed (in addition to have nifti float 32 bit)
- added: unit of voxel size displayed on the image
- added: call of a texture script online directly in LIFEX_start.sh file (Linux OS only) (you can copy/paste the last command line with a different script file on each line)
- added: affine transform of series (S) with aS+b model
- changed: clik&draw and click40% tools now in the Tool menu
- changed: "draw" label menu is changed to "edit" label menu
- changed: the "move" tool selects the reference series automatically and avoids the corresponding warning message
- changed: decrease or increase of + -1 value by step wheel and Shift key pressed (and + -10 with Shift + Ctrl keys pressed at the same time) for snake2D and snake3D tools
- fixed (texture protocol): CONV_minvalue is now calculated
- fixed (MTV protocol): disabling of tools that not available on tool box option
- fixed (MTV protocol): ROI display on 360° angles of MIP
- fixed (MTV protocol): save custom values for pruning (initial & threshold steps) in preference session file
- fixed (MTV protocol): eye always open for maximum values in the sorting criterion menu
- fixed (MTV protocol): numerical sorting for sorting criterion with #id values
- fixed (MTV protocol): closing of the dialog box of sorting menu
- fixed (MTV protocol): artifactual ROI split visible on display
- fixed: rounded values of RTStruct contours are more accurate
- fixed: SUV conversion in Philips proprietary dicom format (formatted as a vector in uint8)
- fixed: round/floor of ROI location (on display) when using absolute or relative threshold
- fixed: threshold when SUV unit is selected
- fixed: optimisation of the memory management when running LIFEx_start.sh on Linux OS
************************************************************
**************** LIFEx public version 4.70 *****************
************************************************************
version 4.70 - Sat Feb 16 18pm CEST 2019
What's new in (feature release) LIFEx 4.70?
- fixed: slice thickness on Biograph_mMR (Siemens)
- fixed (texture protocol): RIM index: proper units (mL and #vx) assigned in excel file.
- fixed (texture protocol): RIM index on some extreme anysotropic voxels
- fixed (texture protocol): RIM index on more than one ROI
- fixed: on mac only, wheel rotation is good direction when 2 finger shift on trackpad (downgrade on jdk1.8.0_144 version)
- thresholding at 40% (and by extension at n%) allowed on the time series. Note that the activated series and the activated time t are defined as reference for the calculation of the maximum value from which the 40% (respectively n% value) is calculated.
- added: image number unit (in #) on X axis (in addition to have sec, min, h units)
- fixed: inopportune flash on MIP movie
************************************************************
**************** LIFEx public version 4.64 *****************
************************************************************
version 4.64 - Tue Feb 7 18pm CEST 2019
What's new in (feature release) LIFEx 4.64?
- updated: memory is better used when launching the application (linux all available memory without buff/cache is used)
- fixed: slice thickness on some CT scan
- added Dsc-MR protocol (not public)
- added (Dsc-MR protocol): read TE and actualFrameDuration from nifti file (not public)
************************************************************
**************** LIFEx public version 4.62 *****************
************************************************************
version 4.62 - Monday Feb 4 10am CEST 2019
What's new in (feature release) LIFEx 4.62?
- fixed: change in the display of the cursor coordinates
- fixed: sorting the series when more than one series is loaded (sorting criterion is « acquisition number » dicom field)
- fixed (texture protocol): Automatic adjustment of relative/absolute intensity resampling menu as a function of the settings already filled
************************************************************
**************** LIFEx public version 4.60 *****************
************************************************************
version 4.60 - Wednesday Jan 30 07pm CEST 2019
What's new in (feature release) LIFEx 4.60?
- added: save screenshot of MIP (png1)
- added: save screenshot of 360° of MIP view (png2)
- added: send screenshot of MIP to booklet (print)
- added: Dicom-REG (registration parameters) reading between two series with different StudyInstanceUID
- added: reading of images in tiff 16 bit format
- added: creation of a new parametric image from a dynamic series: mean of all times, time to peak, time to min, sum of all time images
- added: tissue save format file (dft) of Turku PET Center
- added: tissue save format file with recovery coefficient (dft+rc) of Turku PET Center
- added: Subtraction tool in ROI menu: create a new ROI by subtracting 2 visible ROI (ROI with open eye)
- added: Intersection tool in ROI menu: create a new ROI defined as the intersection of all visible ROI (ROI with open eye)
- added: loading of DICOM-SEG (segmentation parameters) as an ROI file
- added: new rainbow colormap
- added: new transparency on colormaps
- added: warning message when saving dcm files with IOP that are not identity matrix (not yet supported)
- added: Pixel Padding Value (0028,0120) DICOM field supported for CT
- added: possibility to remove the volume corresponding to a given time in a times series
- added: Click&Draw 40% tool added to ROI menu
- added: Dilation of the external edges of a ring ROI
- added: simple operation tools between images
- added: flip tools (R<>L, A<>P and I<>S) operating on images
- added: in linux version only: the available memory of the system is taken into account when launching LIFEx
- added: SUL units
- added: management of image orientation and position coordinates of patient when cor, sag, ax slices are displayed
- added: management of image orientation and position coordinates on viewer
- added: SUVpeak in 0.5mL volume in the result xls file.
- added: bounding box to define regions in which GLCM feature maps are calculated.
- added: Biograph mMR Dicom supported (SharedFunctionalGroupsSequence and PerFrameFunctionalGroupsSequence)
- added: reset all application parameters to default values
- added: software name and version in description tag of nifti ROI, images and MIP nifti written files
- added: warning message if ROI files already exist when a "save ROI" action is run
- added: Dicom screenshot (SOPClassUID) supported
- added: PixelPaddingValue (0028,0120) is used to identify pixels to be excluded from the normal grayscale rendering. It is now supported when reading images.
- added (texture protocol): Local texture map calculation for GLCM indices
- added (texture protocol): PARAMS_BinSize in result xls file
- added (texture protocol): possibility to define bin size value only, without the number of grey level values in the graphical user interface
- added (texture protocol): in the live activity report, (quick) display of the position of each roi while texture processing is on-going
- updated: display order of value voxel on top right of images is now in the same order than list of (layer) series
- updated: improved circle3D and circle2D drawing performance
- updated: crosshair coordinates in image space
- updated: checking and modification of default bound values as a function of the imaging modality for automatic tuning of the display.
- updated: improved loading performance of RTStruct coordinates with multithreading calculation of each z slice
- updated: loading (and also loading over network) now keeps images in data/temporary and not in /tmp in linux system
- updated: enabling of ImageOrientationPatient(iop) and ImagePositionPatient(ipp) when loading Dicom(dcm) et Nifti(nii) images
- updated: enabling of ImageOrientationPatient(iop) and ImagePositionPatient(ipp) when writing Nifti(nii) images
- updated: memory is better used when launching the application (linux all available memory is used, windows 95% of available memory is used, mac os is set to 3.5Go of RAM for 4Go version, 7Go of RAM for 8Go version and 15Go of RAM for 16Go version)
- updated: improvement of the selection of dropdown menus
- updated: MIP nifti file fully saved (before this correction: only every other view was saved)
- updated: "Restore" instead of "Undo" for restore last deleted ROI
- updated: discretization updated to agree with the image biomarker standardisation initiative (IBSI) description
- updated: speed improvement when drawing circle2D and circle3D tools
- updated (texture protocol): Z resampling disabled if 2D images are loaded
- updated (texture protocol): different management of the zero values in NGLDM matrices. Only NGLDM_Contrast and NGLDM_Busyness are affected
- updated (texture protocol): HISTO_kurtosis is shifted by a Fisher correction factor of -3 to have kurtosis equal to 0 for normal distributions
- updated (texture protocol): values expressed in scientific format in excel file results
- updated (texture protocol): discretization in agreement with the image biomarker standardisation initiative (IBSI) description
- updated (texture protocol): LIFEx.texture.SpatialResamplingZ has been changed to LIFEx.texture.ZSpatialResampling (same thing for Y and X) in script file
- updated (texture protocol): unit conversion problem (SUV, #, BqmL) of min and max discretization bounds (in some use cases) now fixed.
- fixed: fields radiopharmaceuticalStartTime and radionuclideTotalDose are set to 0 when reading nifti file
- fixed: automatic window/leveling apply to all modalities
- fixed: RT-Struct reading
- fixed: RT-Struct loading continues even if a ROI structure as no contour (empty ROI are not shown)
- fixed: SUV conversion in Philips proprietary dicom format
- fixed: add message in the web page of the user location map for Firefox navigator : "to view this content with Firefox, you must remove the tracking protection"
- fixed: min and max bounds of relative resampling (min, max, sd) are calculated only for the biggest cluster
- fixed: update of MTV volume when using click and click40% tools
- fixed: dilate/erode tools now work on 2D images
- fixed: update MIP view with use of snake2D and snake3D tools
- fixed: default size window of MIP
- fixed: DICOM-SEG from Olea with IOP and IPP
- fixed: IPP and IOP from DICOM image file with numberOfFrame>1
- fixed (texture protocol): the size of bin is now set to the value of bin size minus one (see the image biomarker standardisation initiative (IBSI) description)
- fixed (texture protocol): in advanced setting, GLZLM_SRE label is modified to GLZLM_SZE
- deleted: Empty button in ROI tools (the « dispose » button does the same)
- fixed: (not public) modification of unit (into cm) of indices in MTV protocol: sumBindCOM, avBindCOM, stdBindCOM, minBindCOM, maxBindCOM, avTotBindCOM
************************************************************
**************** LIFEx public version 4.00 *****************
************************************************************
version 4.00 - Mon Apr 23 12:00:00 CEST 2018
Main:
- save dynamic series in DICOM format
- directory in which data are saved can be changed by the user in preference frame
- not public (mircen, cea): add a late measurement (60min) from a static series at the end of an other time series acquisition (+saving in DICOM format)
- maps of GLCM features are now available
- "diagnosis protocol" has been renamed "Viewer protocol"
- increase in performance when calculating Texture GLCM matrix
Major bug fixes:
- patient position corrected in dynamic time-series
Minor bug fixes:
- correction of timing value (msec) of the last time point in dynamic series
- correction of min and max value units in graph
- MTV: click & draw tool action now updates the MTV value
- hide circle2D and circle3D when mouse cursor exits frame
************************************************************
**************** LIFEx public version 3.74 *****************
************************************************************
version 3.74 - Mon Mar 19 11:00:00 CEST 2018
Main:
- renaming TMTV protocol into MTV protocol
- creation of a DICOMDIR when more than 2 directories are loaded simultaneously, if that file does not exist
- adding of seriesDescription, studydescription and PatientBirthDate dicom tag of a DICOMDIR file
- saving dicom (+anonymised) series in local disk
- nifti ROI loading allows loading multi value ROI in the same ROI file
Major bug fixes:
- sometimes, z shift of 1 voxel on ROI when loading RTSTRUCT file
- fixed artifacts when there were more than 1 contour sequence by slice in RTSTRUCT files
Minor bug fixes:
- now, release annoucement frame is not a modal frame
- texture: improved management in script execution when binSize=0 and nbGreyLevel=0
- texture: NGLDM_Busyness formula has now an absolute value at the denominator
- loading of coronal DIXON MR images with more than one contrast in the same series
- loading nifti-1 file when imagePositionPatient is not null
- texture: inversion in output xls file (optional) between rows and columns of the grey-level zone length matrix (GLZLM)
- improved tuning of the size of the menu windows as a function of the screen resolution and size
*********************************************************************************************
****************************** LIFEx public version 3.64 ***********************************
*********************************************************************************************
version 3.64 - Tue Feb 08 17:08:00 CEST 2018
Main:
- addition of translation of image layers with respect to the locked reference layer
Others:
- ending (and unselect tool) of ROI edition (circle2D, circle3D, Pensil2D) when pressing the "e" key on images
- (not public) TMTV: display of total MTV in each quarter separately
- texture: addition of parameter LIFEx.texture.GLCM.DistanceWithNeighbours=n in script file
- texture: text field of BinSize is now enabled when relative intensity resampling is selected
- addition of a message when the DICOM field studyInstanceUID of a new series that is loaded is not equal to the studyInstanceUID of the reference scan already loaded
- ROI move button is now enabled in tool manager on PT modality
- color of first ROI is now magenta (green before) for increased visibility
- (not public) TMTV: addition of cross section coordinates (coronal: x, z) in the result xls file
- (not public) TMTV: addition of the number of ROI in result xls file
- (not public) TMTV: addition of avTotbindCOM in result xls file
- (not public) TMTV: highlight (in red) of min and max value in each column of the result xls file
Major bug fixes:
- inversion Inf<->Sup on ROI when loading RT-Struct file
Minor bug fixes:
- TMTV protocol is now possible with series in NIFTI-1 (nii) format
- ROI creation is possible even after series in NIFTI format is loaded
*********************************************************************************************
****************************** LIFEx public version 3.56 ***********************************
*********************************************************************************************
version 3.56 - Tue Jan 23 17:31:00 CEST 2018
Main:
- loading of RT-Struct on reference layers other than LIFEx reference layers (first loaded series) is now available
- TMTV: addition of fast labelling of ROI with selection of names in a predefined list of names
- (not public) TMTV: addition of cross section to define quarter labelling relating
- (not public) TMTV: assignment to each ROI of a reference quarter in coronal plan
- (not public) TMTV: labeling of each ROI as a function of the region it belongs to
- (not public) addition of the ROI center of mass (COM), sumCOM, meanCOM, minCOM, maxCOM of distances between ROI COM in the results excel file
- addition of a new protocol called "Diagnosis" corresponding to a simple viewer protocol without any complex functions
- addition of 6 new display options (template 1 to 6)
Others:
- Texture: CheckTex button is enabled only if texture protocol is selected
- Alphabetical sorting has been added to sort ROI layers
- AcquisitionNumber DICOM tag is now taken into account for the CT modality
- Addition of the coordinates (vx) of the voxel including the MaxValue within the ROI into ROI information
- Automatic setting of a default color map and alpha value to 0.5 when a second series is loaded
- Automatic setting of a default window/leveling based on the histogram of the loaded volume
- Creation and opening of a DICOMDIR file when 2 folders are loaded simultaneously, if that file does not exist.
- management of DICOM tag: imageRotation with an y inversion
Minor bug fixes
- Texture: the RT-STRUCT loading is now supported when using scripts
- TMTV: MIP ROI color is changed when ROI color is changed (dialog box of ROI)
- TMTV: existing MIP is fully loaded (while only every other angular views were loaded before)
- TMTV: % threshold is now in SUV "unit"
- Management (hide/show) button in ROI manager window
- Graph units now defined in the histogram image