The latest version is version 4.00


**************** LIFEx public version 4.00 *****************
version 4.00 - Mon Apr 23 12:00:00 CEST 2018

What's new in LIFEx 4.00?

- save dynamic series in DICOM format
- directory in which data are saved can be changed by the user in preference frame
- 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

What's new in (feature release) LIFEx 3.74?

- 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 ***********************************

What's new in LIFEx 3.64?

- addition of translation of image layers with respect to the locked reference layer

- ending (and unselect tool) of ROI edition (circle2D, circle3D, Pensil2D) when pressing the "e" key on images
- 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

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

What's new in LIFEx 3.56?
- 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
- 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)

- 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

****************************** LIFEx public version 3.42 ***********************************
version 3.42 - Fri Dec 15 17:31:00 CEST 2017

What's in LIFEx 3.42?
- Texture: renaming of textural indices, e.g: Homogeneity of GLCM matrix become GLCM_Homogeneity
- Texture: increased precision of textural indice results (float->double)
- Texture: moving CONV_volume to SHAPE_volume in the xls results file
- Texture: absolute and relative resampling intensity also applies on first order indices (previously, relative resampling was systematically used for first order indices)
- Texture: new HISTO_entropy with log2 formula (HISTO_entropy_log2)
- Texture: new GLCM_entropy with log2 formula (GLCM_entropy_log2)
- Texture: new checkbox in advanced parameters of texture panel for saving values histogram in excel file
- Texture: when a ROI includes several clusters, the histogram is calculated using all cluster voxels while texture indices are calculated for the largest cluster only

- Main: removal of the validated/advanced levels in first windows (advanced is selected by default)
- Main: emoval of modalities choice (all modalities are selected by default)

Bug Fixes
- Texture: Correction of an edge effect in the GLCM
- TMTV: Liver value shown in the dialog box to set a threshold as a function of that value is now expressed in SUV units
- Main: modification of problematic slash into PatientID, PatientName, StudyDescription, SeriesDescription and SeriesUnit DICOM fields when saving image in nifti-1 file
- Main: reordering temporal images with the InstanceNumber field when the ImagesTime field is null on DICOM files

****************************** LIFEx public version 3.40 ***********************************
version 3.40 - Thu Nov 09 11:30:00 CEST 2017

What's in LIFEx 3.40?
- improved memory management of the main application (mostly useful for running scripts)
- export of texture results in comma-separated values (csv) format file
- saving indices and texture parameters to be calculated from one work session to another

Bug Fixes
- random stalling of texture scripts
- long ROI name (>31 characters length) are now supported when saving results of texture protocol in an xls file
- default voxel distance for texture protocol is 1 vx (against 2 vx for the 3.38 version)

****************************** LIFEx public version 3.36 ***********************************
version 3.36 - Thu Oct 26 18:30:00 CEST 2017

New software features:
- it's now possible to reorder layers of series to display them in any order

- error message is now displayed when texture input fields are not correctly defined
- fixed bug: error "The pixel size (x, y, z) of reference series must be smaller than the pixel size of selected series"

Miscellaneous, fixed and checked issues:
- the "null" value possibly assigned to the studyDescription DICOM field of the images no longer produces an error when saving nifti-1 file series
- restoring the view of "BirdEyeView" on Ax, Sag, Cor frame tools
- fixed bug: saving ROI in nifti-1 file series with proper "n+1" magic number in the header
- fonts and window size modified to adapt to low screen resolutions (<= 1280x1024 pixels)
- fixed bug: setting a ROI onto the 2D image with circle2D and snake2D tool
- new zoom cursor not as sensitive as before for easier handling.
- adding the fonts (bold, plain) on log file to debug

****************************** LIFEx public version 3.30 ***********************************
version 3.30 - Wed Sep 20 11:39:00 CEST 2017

New software features:
- possible setting of the voxel size in which textural features are calculated in texture protocol
- management of multi-series with common ROI

File handling:
- PET images displayed in Bq/mL Units when conversion into SUV unit is not possible (missing Dicom fields)
- fixed bug: modification of problematic slash into PatientName DICOM field when saving results of texture protocol in an xls file
- fixed bug: oblique images now properly displayed when "orientation matrix » DICOM field is not null

Algorithms and utilities:
- refinement of the ROI position to calculate SUVpeak in PET: difference ≤ 0.01 between new SUVpeak compared to the one calculated in previous LIFEx regions

VOIs and paint:
- fixed bug: error in displaying ROI statistics when multi-series were loaded simultaneously
- fixed bug: Nestle ROI calculation was refined
- new tool: ROI erosion with defined voxels or spacing
- new tool: ROI dilation with defined voxels or spacing
- pencil2D tool: increased line width and added color at drag handle point. The Press "e" option was introduced to close (end handle point) ROI

Images and paint:
- change in maximum zoom factor of displayed image: images can be zoomed 4 times more
- addition of a low/high switch for quality rendering on images canvas with pressing the "s" key
- display of the position and value of the cursor for each loaded image series

- addition of a saving option (xls format) of the diplayed histogram values
- texture script are no longer stalled when a MIP view has been displayed
- removal of the empty row between title and values in the xls texture files
- addition of the SeriesDate field in the xls texture files

Miscellaneous, fixed and checked issues:
- correct setting of the ROI when displayed on an image series different from the one that was used to create the ROI
- cleaning a some stalled information messages

- UserGuide \ Nestle Segmentation, p.33: V (threshold) is changed into T (threshold) for clarity
- UserGuide \ tools GUI: Addition of the dilate/erode tools help
- AppendixTexture: Addition of the multi-series management


****************************** LIFEx public version 3.12 ***********************************
version 3.12 - Fri Mon 26 15:00:00 CEST 2017

Major changes:
- new main features added in this version: no, minor version

Fixed and verified issues:

File handling:

Algorithms and utilities:

VOIs and paint:
- fixed bug: after using the 2DSnake or 3DSnake tools, the displacement across slices using the (up, down) key was no longer exactly 1 voxel.
- fixed bug: drawing or loading ROI was impossible after reading nifti-1 file series




****************************** LIFEx public version 3.10 ***********************************
version 3.10 - Jeu Jun 21 15:00:00 CEST 2017

LIFEx v3.10 now available
LIFEx reads DICOM images locally or over a network using a DICOM browser,
is compatible with Osirix and includes a powerful 3D reconstruction-based slice viewer.
Volume of interest (VOI) can be either imported from previously created files or drawn and manipulated using LIFEx.
Results are exported in Excel format files. LIFEx runs on Windows, MacOs and Linux.
It is distributed with examples and includes a tutorial.
User support is offered. Users can optionally contribute to the gathering of index values in different tissue types and different images as a public data bank of reference values is currently being built and integrated to the software for assisting the users with the interpretation of their results.

This release includes:

Major changes:
- new main features added in this version: Maximum Intensity Projection (MIP)

Fixed issues:
- automatic calculation of textural features using scripts for multi-patients and multi-ROI / patient data (see documentation)
- new feature added in texture script: setting nbGreyLevels=0 for automatic calculation of the number of grey levels from the binSize parameter when relative discretization is used
- new feature added in texture script: setting binSize=0 for automatic calculation of the bin size from the nbGreyLevels parameter when relative discretization is used
- new feature added in texture script: loading of all script files at the same time (drag and drop) that will then be executed sequentially
- fixed bug in the erosion process
- fixed color coding when inverting the black and white colormap
- fixed ROI split tool to account for all voxels in the initial ROI.

File handling:
- a Philips DICOM bug found into old images that impacted SUV; (0x70531009 & rescaleSlope had identical value and scaling was performed twice in the conversion in SUV)

Algorithms and utilities:
- acceleration of ROI processing when multi layers of series are used

VOIs and paint:
- fixed "show/hide all ROI tool" when the button was used twice in a row.
- fixed update histogram and curve values when using the "show/hide button"
- improvement check tool "CheckTex" for good parameter ROI for texture processing (before script, it can be a step of validation) je ne comprends pas. En français ?
- add KeepOne tool for keep only the largest ROI (=split tool, with one ROI result)
- add Window/Leveling threshold ROI tool
- add fill3D ROI creation tool by filling "holes" in another ROI (example, lung fill) by clicking on a voxel within the hole that should be taken as the seed point.
- 3D and 2D snake tools are now available within all modalities, when multi-series have been loaded and for all protocols
- the reading of a ROI that has not been drawn on the loaded patient is now possible. The ROI shape is preserved but not the location in the image.


- texture documentation now includes explanation regarding the use of script for texture calculations

****************************** LIFEx public version 3.00 ***********************************
version 3.00 - Fri Mar 17 15:00:00 CEST 2017

Major changes:
- new main features added in this version: MTV protocol

Fixed and verified issues:

File handling:
- Fixed and warning message concerning null value of SerieDate DICOM Field (0x00080021) need for SUV conversion
- Fixed and warning message concerning null value of SerieTime DICOM Field (0x00080031) need for SUV conversion
- Patient name is get and set from filename when loading a nifti (nii) files

Algorithms and utilities:
- New (total) Metabolic Tumor Volume Protocol as named : "MTV protocol"
- Improvements: MTV protocol - separatly of cluster in new ROIs after all thresholds
- Improvements: MTV protocol - viewing / editing of step1 calculation
- Improvements: Texture protocol - the distance of neighbours in GLCM is now available
- Improvements: Texture protocol - a new intensity range normalisation quantization method is available: resampling is performed in the range defined by mean+/-3sd of intensity values in the ROI
- Improvements: Texture protocol - date of processing (multi patient processing) is displaying in a new column and not in one line as before

VOIs and paint:
- Tool to measure angles is available on coronal and sagittal planes in addition to axial plane
- Tool to measure distances between two points (ruler) is available on coronal and sagittal planes in addition to axial plane
- Tool to pencil2D is available on coronal and sagittal planes in addition to axial plane
- Fixed minor bug in translate/snake2D/snake3D tools
- Fixed minor bug in circle2D/circle3D with multi ROIs overlapped
- Fixed loading nifti ROI files with no compression (.gz was already ok)

- New features: possible selection of several protocols in a single run
- Fixed: Open of advanced paramaters frame (Texture protocol)
- Fixed: Addition of warning message when no protocol selected in the first frame
- Fixed: New version available frame is now always on top of screen
- Improvements: addition of tutorial video of MTV protocol

- Fixed: Texture protocol documentation - formula to be used for the calculation of GLCM matrix corrected
- Add tutorial movies to learn MTV protocol


****************************** LIFEx public version 2.20 ***********************************
version 2.20 - Thu Jan 17 10:54:00 CEST 2017

Important warnings:
- Following a modification of orientation in the recording and reading of ROIs stored in Nifti in LIFEX 2.20, all ROI files recorded using a previous version should be flipped in the left-right direction and in the anterior-posterior direction after being read
-- Flipping tools L<>R and A<>P are provided in the ROI toolbox
-- The flipped ROI should be saved so as to avoid having to repeat the flip operations each time the old ROI file is open

Network handling:
- Fixed: "No images found" error message when connecting to the DICOM server

File handling:
- Drag and drop image files from file system to series area of LIFEx
- Improvements: value -32768 on DICOM DataBufferShort detected an as error and set to 0
- Corresponding warning message in GUI: n voxels with value -32768 have been set to 0
- Improvements: reading/saving of images in Nifti-1 format (.nii) implement SUV and UH units (cf. filename)
- Fixed: directories and names of saved images (.img, .nii) are corrected on Windows OS
- Improvements of reading images in Nifti-1 format (.nii): Double and Float types are now supported
- Fixed: new Orientation of CT images in Nifi(nii) format files
- Fixed: ActualFrameDuration DICOM field can now be read with the scientific format (E+00)
- Removal of the preview of the "FileChooser" window which introduced a bug in windows10 and windows8
- Fixed: Orientation of the Patient Image in Dcm format images (Cor, Sag)
- No longer supported feature: the Analyse format file (.img+.hdr) is no longer supported
- Solved: FileChooser window random display using Windows10 and Windows8

Algorithms and utilities:
- Fixed a bug in relative resampling of Texture protocol (without impact on previous results)
- The TI of normalized GLCM calculated in each direction can be saved in a csv file

VOIs and paint:
- New tool for ROI sorting (as a function of SUVmean, SUVmax, Volume)
- New flip tools (existing R<>L, new A<>P and I<>S)
- Fixed Orientation Image in RT-Struct ROI
- Improvements: no load of ROI files on startup
- Improvements: Drag and drop ROI files from file system to ROI area of LIFEx

Image views and visualization:
- Optimization of images display (faster display)

- Fixed: a bug affecting the position of images tools on Mac OS
- Fixed: all temporary images are now deleted when exiting the application

****************************** LIFEx public version 2.00 ***********************************
Tue Sep 13 15:42:00 CEST 2016

New Features:
- enhanced Graphical User Interface to facilitante the use of the software
- new positioning of some command buttons to make them compatible with the touchscreen feature of new laptop devices.
- reading of TIFF, JPEG, PNG, BMP image format
- reading/saving of images in Nifti (.nii) format
- new tool to measure angles
- new tool to measure distances between two points (ruler)

- reading of DICOM images in which many of the DICOM fields useful for nuclear medicine scans were removed (such as the DICOM "radiopharmaceuticalInformationSequence" including the radiopharmaceuticalStartTime, radionuclideTotalDose, radionuclideHalfLife fields)
- more flexible DICOM-RTStruct reading, with the possibility of reading files with a ReferencedSOPInstanceUID of the RTStruct files different from that of the loaded images
- the RTSTRUCT modality is active by default, so that regions can be read from external files without changing the default settings
- only two operating modes are now proposed: the "Validated" and "Advanced" modes
- automatic selection of the draw2D toll when creating an ROI from a 2D image
- checkbox for YES/NO output textural matrix files (no output by default)
- array transpose of result (Excel file)

Fixed bugs (or others):
- fonts and window size modified to adapt to HD screens (>= 3200x1800 pixels)
- documentation and tutorials updated to include the new graphic layout
- help messages associated with a tool remaining open when a new tool was selected are now removed
- deactivation of activated ROI-associated tools when an ROI is closed
- non closing of the browser used to read images when a patient folder is closed
- optimized pointer and line sizes as a function of the FOV of reference images
- "info DCM" tool inactivated when OTHER modalities are used (bmp, tif, jpg, png, gif, nii, img)
- 3D tools inactivated when 2D images are used
- create PDF of booklet is now located in patient/screensave/pdf directory (windows version only)
- error message "DICOM Tag location = 0 : ERROR" corrected on CT images
- JPGEG2000 Compression library on Windows operating system

****************************** LIFEx public version 1.83 ***********************************
New Features:
- minor release, no new feature
- on request only (under password): calculation of K1, k2 and Ki using a 2 tissue-compartmental model (plasma + tissue)

- enhanced presentation of the conventional ROI metrics (mean, max, min, standard deviation)
- textural matrices now saved in cvs format in the file directory

Fixed bugs:
- closing of all windows when uploading data from a new patients without having to quit the application.

****************************** LIFEx public version 1.82 ***********************************
New Features:
- minor release, no new feature

- Image (Lecture) :
- The "null" value possibly assigner to the SOPInstance DICOM field of the images no longer produces an error.
- The ImagePositionPatient DICOM field of the image series is accounted for when reading RT_STRUCT objects.
- Texture :
- The code for calculating the GLCM matrix has been parallelized.
- Textural parametres are saved from one session to another.
- The histogram is displayed for all ROIs in a same plot.
- ROI :
- Management of RTSTRUCT corresponding to images with a specific DICOM ImageOrientationPatient value.
- Management of the RT-STRUCT files when they are in the same directory as the associated images.
- Displacement of the 3D views based on the coordinates of the ROI maximum value when a layer is activated, so that the ROI is automatically visible in the display window.
- Simulatenous opening of several ROI (in nii format) using a single multiselection.
- Layers corresponding to intermediate ROI drawing steps in the Neste method are now deleted.
- The color of new ROI is now based on the color of existing ROI when the new ROI is derived from an existing one (for instance when using a copy or mirror operation).
- Display of the volume value (in cm3) when using the 2D disk and 3D disk segmentation tools.

Fixed bugs:
- correction of a message regarding cluster number > 1 on 2D slices and some 3D slices
- correction of the "Not a Number" error displayed when texture results were added in a "TextureSession.xls" session file
- position of the "curve" or "TAC" window now saved in the session preference.
- debug of the US reading for THOSHIBA TUS-A500 and SuperSonicImagine scanners.

****************************** LIFEx public version 1.8 ***********************************
New Features:
- US b-mode modality is now implemented and fully supported for reading static/dynamic images.
- US Elastography of SuperSonicImagine is now implemented and fully supported for reading static images.
- US QualityMap of SuperSonicImagine is now implemented and fully supported for reading static images.
- Texture indices are calculated in a ROI for one or several layers (1 layer = 1 image series).

- no calculation of ROI TLG value when processing CT and MR images.
- no automatic ROI saved (to nifti format) if rename it.
- the use of a session file storing results obtained in several patients is now implemented.
- displaying float images with max values of 1.00 is now implemented (ex. US quality image).
- properties files now located in the user home directory.
- add a display window to choose the colormap of images series.

Corrected bugs:
- some DICOM-MOVE request errors have been fixed.

****************************** LIFEx public version 1.71 ***********************************
- the 2D painting tool is available

****************************** LIFEx public version 1.7 **********************************

New Features:
- minor release, no new feature

- faster calculation of GLCM, NGLDM, Sphericity, Histogram-based index, and conventional index calculation using parallel threads.
- faster calculation of GLZLM using parallel threads (iLevel).
- faster calculation of GLRLM using parallel threads (iDirection).
- no calculation of ROI peak value when processing for CT and MR images.

- distribution of tar files instead of zip files to handle all execution permissions of files under linux

- the "Radionuclide Total Dose" field is displayed only when its value is greater than 1 (Not in CT, MR images)
- the "Number of grey level" and "size of bins" values are now in integer format

****************************** LIFEx public version 1.65 ***********************************
New Features:
- minor release, no new feature

- texture: the minimum number of grey levels is set to 1 (textural processing)
- optimization of the values displayed in the information box of ROI
- the diameter of the sphere used for the close operation is set to 20 mm instead of 10 voxels
- the threshold can be expressed as a range bound by a min and a max values in the ROI


- extraction of multiple patients is implemented in a same DICOMDIR file
- after loading an RTSTRUCT object, calculation of the ROI size even when the ROI name of the RTSTRUCT object is null

******************************** LIFEx public version 1.6 **********************************
New Features:
- DICOM-RTSTRUCT is now implemented and fully supported for reading ROI only (not writing RTSTRUCT)
- DICOMDIR is now implemented and fully supported for reading DICOM images only (not writing DICOMDIR)
- threshold at n% of max value of ROI

- the dialog box now keeps in memory the path to the file that has been previously read.
- PT icon has been changed to a PET icon.
- verification of authorized operating level with RTSTRUCT modality activated or not
- new shortcut: when you click on the "Please select one or several imaging modality(ies)" header of the initial LIFEx menu, all modalities are activated.
- ScrollPane added on the panel serie of the main frame
- button of load RTSTRUCT added in the dialog box of ROI management
- button of load (analyse, nifti) ROI formats added in the dialog box of ROI management
- increase in performance calculations of the maximum values (SUVmax...)

- on windows version, setting of 95% of the free memory as the maximum memory busy from LIFEx.

- offset correction of the 2D & 3D painting tool relative to the mouse cursor on thick slices with a high anisotropy of voxel.
- correction of message "The bin value is not defined or cannot be smaller than 5" for MR images.

******************************** LIFEx public version 1.5 **********************************
February 17th, 2016
- error in the version number on the Windows version.
- on windows version, setting of 80% of the free memory as the maximum memory busy from LIFEx.
- ScrollPane added on the panel series.

******************************** LIFEx public version 1.4 **********************************
February 17th, 2016
- WIN: transformed from 64B with the available memory to 3GB (now bigger CT and saving ROI are allowed).
- GUI: DcmBrowser -> GUI for editing "New Node" is added.
- GUI: DcmBrowser -> selecting one series from the network is added.
- TEX: reviewing textural inputs to add minimum bound for resampling CT scan.
- MAC: new release of version 1.3 is available.
- TEX: CT histogram with negative values is added.

******************************** LIFEx public version 1.3 **********************************
February 15th, 2016
- PRO: close button on window "Choose protocole" added.
- TEX: +abs(minValue) on CT texture matrix added.
- LIC: changes in section 13 of the license.
- MAIN: low memory display on load deleted.

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