PMOD Software Release

Notes
Version 3.7

PMOD Technologies

Printed on 22 August, 2016

2 PMOD Software Release Notes

PMOD Software Release Notes

Maintenance Builds of Release 3.7

Build 9  PNEURO: Optional background VOI added for use in partial-volume correction.
August 22, 2016  PNEURO: Selection of the model for mapping fixed when retrieving protocol.
 PSEG: Bug fixed in the LMA PVC when using the Clustering method.
 PKIN: t* in MRTM0 was not correctly handled.
 PCARDP: Different internal handling of the interpolation, because the RAM
demand was excessive for small animal data.
 Database loading: Fixed issues (selected series, timing) when loading from a
transaction server with selection.

Build 8  Absolute values for MIP projections supported.

July 23, 2016  Wistar Rat Atlas (Tohoku) added.
 PSEG: Cluster analysis extended to use a set of external TACs as clustering
centroids.
 PSEG: Background removal revised.
 PKIN: Display of the weighted residuals changed from r/sd^2 to r/sd. Doesn't have
an impact on the calculations.
 Fuse It: Modality dependent display configuration added.
 Improved loading of multiframe TIFF images.
 Installation from command line without GUI:
java -jar setup.jar -quiet "D:/"

Build 7  VOI: Volume of hypoxic voxels added to the statistics measures.

April 29, 2016  Calculation of TAC timing for scanners with continuous acquisition mode
updated.
 PCARDP: Polar sampling improved for the case of myocardium definition by
endo/epi outlines.
 Interpolation tool: Explicit options (other than the default mirroring behavior) to
handle extrapolation outside the volume boundaries.
 SUV display switch: The SUV conversion was applied even in the case of values
already in SUV.
 Facility to generate an R server starting script from the Config panel.
 R: Assigning condition to a variable by the "Set" function improved.

Build 6  PNEURO: Parcellation can be deactivated.

April 7, 2016  PXMOD: Cardiac perfusion model for ammonia has a new masking option. The
hardwired (vLV+vRV)>0.75 criterion is replaced by an explicit threshold.
 PCARDP: The MBF parameter image is now also masked when applying Epi/Endo
segmentation.
 PCARDP: contour detection in the gated images improved.
 PMOD Software Release Notes 3

 VOI: Improvement of a slight problem in pixel classification when interactively

defined vertices were exactly at voxel corners.

Build 5  DB structure adjusted for better support of multiple parallel clients on a single
March 8, 2016 computer (eg. ATL version on a single server). Verification of DB versions added
to automatic check. Note: Existing databases may need upgrading via the DATABASES
tab on the "Config" tool after installation of Build 5.
 New server manager functionality. The manager user interface can be started by
adding the "-admin" argument in the RunPmod script. It allows
starting/stopping/monitoring the server processes (DICOM, database, license
servers), viewing logs and outputs, and freeing ATL licenses. The server manager
doesn't consume a license.
 There was a problem with WIBU key access when exiting sleep mode. Improved to
avoid PMOD shutdown.
 Distribution: Java VM updated to 1.8.0_73.
 VOI: Interpolation between B-spline ROIs results in B-splines.
 VOI: Two options for calculating the Peak VOI results: using the full sphere, or
only the intersection of the sphere with the original VOI.
 R: Improved handling of NaN values in the basic statistics scripts.
 R: Functionality to edit aggregate values and apply arithmetic operations to them
added.
 R: Extraction of external covariates introduced.
 PKIN: User interface for a second input function (metabolites) removed, which
was not used.
 PKIN: AUC of the "Residence times" model was wrong if integration from time 0
was enabled. Additional slight improvements.
 PKIN: Fix for km files created from PCARDP.
 PNEURO: "Save all" option extended to include protocol saving.
 The same default parameters for tissue probability maps normalization are used in
all tools (same as in PNEURO).
 The replace tool now supports NaN as the replacement value.
 PCARDP: RV region is now outlined closer to the LV. Cropping avoids truncation
of any defined VOI.
 PGEM: PICO probabilistic tracking method added. Requires tensor image
calculated in PXMOD with LUT option and saved in database or as DICOM.
 DICOM: The "Accumulated counts" information is preserved when saving images
as DICOM NM objects.
 Patient information can be edited when importing DICOM data into a database,
and when copying data between databases.
4 PMOD Software Release Notes

Build 4  VOI: The mirror operation can now be combined with cloning of the original VOIs.
Dec. 21, 2015  VOI: Transformation with the deformation field from the 6 probability maps
normalization is now also supported.
 VOI: Improvement of RTSS export. Exclusions are handled in a DICOM-compliant
by introducing bridges.
 PKIN: Residence times model could fail when the exponential integration didn't
start from time 0.
 PKIN: Vt was added to the 3-Tissue Compartment Model. A model variant with
K1/k2 as fit parameter is added.
 PXMOD: The LSRTM model returns NaN instead of 0 for outliers.
 PCARD: The gated analysis now includes 17-segment results.
 Segmentation: Option added to adjust the standard brain mask to the data (using
normalization of a brain template to the input image).
 Font size extended to 32 for supporting displays with very high resolution.
 Configuration: Alphabetical sorting supported for configuration lists, like models.

Build 3  VOI: Change of the hypoxia index calculation in fraction mode. Now only pixels
Nov. 20, 2015 with at least 50% VOI inclusion are used.
 PNEURO brain norm editor: Automatic cropping added.
 PNEURO Batch mode: Hammers 1mm was not supported properly. Warning
message added indicating that only the 4 standard atlases are supported.
 PXMOD, P3D, PVIEW: Brain extraction now also working on DWI MR data.
 PKIN: LSRTM model had not been included in model list.
 Gated PET: Automatic valve plane fitting improved. Use of an explicitly defined
maximum value in polar plot switched off per default.
 Philips par/rec data: Loading improved for 4D flow data.
 Transaction server: Loading speed improved for multi-file images.
 Transaction server: Issue solved when saving to a 3.7 database from a pre-3.7
installation.

Build 2  Transaction server: backward compatibility and stability improved.

Nov. 6, 2015  PNEURO: Affine initialization for 3 probability maps segmentation by overlap
method.
 PNEURO: Transfer of multiple parametric maps to Fuse It.
 PXMOD: handling of RGB maps and failures in "Save all".
 VOI: Choice for the plane orientation when outlining atlases.
 VOI: Fix of the "Group" statistics results in the presence of contour and atlas VOIs.
 VOI: Fixes in the calculation of statistics for probabilistic VOIs.
 PGEM: Protocols for the tracking applications improved.
 PCARDM: Fix in linearity correction and protocol saving/retrieving.
 Fusion display: tooltips for the tabs indicating which images are mixed.

uild 1 Initial upload of 3.7 version.

Oct. 26, 2015
 PMOD Software Release Notes 5

Product Release 3.7

Along with many general improvements, the 3.7 product release extends PMOD to new application
domains. A new PXMOD model calculates parametric diffusion maps and the diffusion tensors from DWI
MR images. Further processing of the tensors and tractography is supported by the PGEM tool. In a similar
manner, PGEM is able to calculate and visualize streamlines derived from MR 4D flow images. The cardiac
tools are extended by functions for the analysis of gated data, both from humans and animals. Following
up on requests from scientists developing new tracers, support for the analysis of dosimetry image data
has been added and arranged in a smooth workflow.

Features

General  Thorough use of NaN values ("not a number") to indicate results and pixel values
which are not valid (PKIN, PXMOD, PNEURO, Fuse It). Formats supporting float
values preserve NaNs. In DICOM objects NaNs are stored as padding values.
NaNs are disregarded in statistics.
 Merging of static images into a dynamic series now supports decay correction.
This convenience allows correcting separately acquired statics as occurs in
dosimetry studies to the same time point.
 For PET data, the display units can be switched between kBq/cc and SUV.
 Support of predefined window settings for the configured color tables.
 Revised communication between transaction servers resulting in more reliable and
faster connections.
 External tool added for reading DWI MRI gradient information.
 Curve units handling improved.
 Image capture into a DICOM series now possible in all directions, not only z-
plane.
 Revised handling of the origin when the pixel size is changed: The location can be
set to the center, stay at the same anatomical location, or the origin values can be
retained.
 Simplified addition of an existing database to the list of data sources.

VOI  Automatic PET Tumor volume segmentation method implements which is

independent of the signal-to-background ratio. (Jentzen W: JNMT 2015).
 The fractal VOI shape dimension can be calculated.
 In addition to transferring the VOI average TAC to PKIN, the individual pixel
TACs can be transferred.
 A timing offset can be added to the TACs from data with multiple table positions,
depending on the VOI position in the volume.
 Support for probabilistic atlases which specify the VOI probability per pixel
instead of a clear delineation.
 An option was added to automatically back up VOIs at regular intervals.
 Organ lists for dosimetry purposes added with assigned volume and mass.
 Basic support of Osirix csv VOIs. The files have to be renamed to *.voi.
 Option to triangulate the planes in the VOI center instead of the first slice when
6 PMOD Software Release Notes

double-clicking into the VOI list.

 SUV unit is serialized in the statistics viewer.
 Histogram display of multiple VOIs improved.
 Histogram of pixel values can be displayed when iso-contouring in a VOI.

PGEM Complete revision of the tool and extension by new functionality.

 Loading of diffusion tensor images and fiber tracking with various methods and
restrictions.
 Loading of MR 4D flow images and calculation of streamlines.
 3D visualization of fiber tracks or streamlines.
 Saving of fiber tracks or streamlines as VTK files which can be used for
visualization in other programs (e.g. ParaView).
 Generation of dynamic PET phantom images based on a VOI atlas and
corresponding TACs.

PNEURO  6-probability maps normalization added (corresponds to the segmentation-based

normalization in SPM12).
 Volume modulation option added when generating the normalized MR in the
atlas space. The results can be used for brain morphometry.
 Mapping part extended by adding the VOI & Fusion tab as in PXMOD.
 Transfer of dynamic input data and resulting parametric maps to Fuse It for
comparison.
 Norm editor supports segmentation and volume modulation.
 Species support for the Maximum Probability approach.
 Parcellation now generates the same cortical areas as Maximum Probability. A
different normalization has been used before.
 Skull stripping added as a new option for rigid matching.
 A warning icon is shown when non-standard definition of the grey/white matter
segments are used.
 Addition of the DTI model for calculating diffusion maps.
 PMOD Software Release Notes 7

PFUSEIT  6-probability maps normalization added. Resulting deformation maps can be

saved.
 Masks supported for probability maps normalizations.
 Triple fusion page added.
 "Primate" added as an additional species for settings configuration.
 External tools enabled for Reference and Input data.
 Batch improvements: Saving of job lists; use of pairing to simplify configuration.
 Volume modulation (preserve total amount) option introduced for reslicing, in
case an elastic transformation is applied. Required for morphometry.
 Fusion balance buttons activate the corresponding image tabs.
 Scientific capture added.
 Support for NaNs in image algebra.
 Interpolation settings of reslicing are serialized between sessions.
 Landmark setting problem fixed when the image was zoomed.

PKIN  An optional blood volume correction was added to non-compartment models

(Logan, Patlak, MA1, MA2, Bolus/Infusion, Plasma Ratio, Tracer Retention). For
blood volume fractions >0 the whole blood contribution (frame average) is
subtracted before the actual analysis. Note that data saved with these modes is not
compatible with prior versions.
 Three irreversible models added. Two of them support the Flux as a fitting
parameter, which can be initialized from the Patlak plot. The parameter lambda*k3
is also calculated.
 Revision of the "Residence times" model, supporting standard organ volumes.
Function to export the results as an OLINDA/EXM case file.
 Introduction of a taskbar containing the most useful fitting options as well as
model filter presets. A "?" supports tab-sensitive helps.
 When the conversion flag is enabled during model switching, the vB, t* and Flux
parameters are also copied among the relevant models.
 Loaded blood measurements can be replaced by the interpolation function values.
A new plasma activity curve can be generated from the resampled input curve.
 A deconvolution methodology for dispersed blood data acquired with online
sampling systems has been implemented (Munk et al, Med Phys 2008).
 It is not any more required that all regional TACs have the same timing. For
instance, in dynamic whole-body acquisitions there is a time offset between
different parts of the body.
 The TACs of individual VOI pixels can directly be transferred to PKIN. Up to
10'000 TACs are supported.
 The result of the Runs Test is returned as a p-value rather than a binary.
 Monte Carlo simulation support added for non-compartment methods with TAC
as target (MLAIR, MRTM, MRTM2, LLSQ) as well as non-TAC targets (Logan,
Patlak, Logan Ref, Patlak Ref). For the latter, noise is added to the measured TAC.
 Composite file format extended for incorporating demographic information.
 Blood data can also be modified using the "Edit data" window.
8 PMOD Software Release Notes

 Direct transfer of kinetic parameter sets (.kinPar) to R without the need of

aggregating them first.
 Use of parameter names instead of the parameter index in .km files. This means
that 3.7 PKIN files are not compatible with older installations.
 The initialization, conversion and random fits options are also supported in batch
mode.
 Better handling of curve units for non-radioactivity data.

PCARD  Workflow for the analysis of gated series added (PET and MR).
 CT perfusion workflow added.
 Cropping changed from cube to ellipsoid.

P3D  Reduction percentage of the number of surface triangles introduced. Speed can be
improved and the object size decreased without notable surface degradation.
 Visualization of tracks such as DTI fiber tracks and 4D Flow streamlines.
 Visualization of vector fields such as the deformable matching deformation field.
 Morphological closing option added to the segmentation process.
 Better support for covariates in the LME script.
R Statistics
Console  Automatic parsing of VOI name suffixes (_l, _r) and generation of a condition
vector Left, Right, Other.
 Polar plot visualization added.
 Script added for the analysis of MR relaxometry data.
 Loading of curves added.
 Support for saving of tables as result files and their aggregation.
 Report now includes patient information.

PXMOD  A model was added for the analysis of DTI MRI images. It calculates various
parametric diffusion maps as well as the diffusion image tensors, which can be
used for fiber tracking. To accommodate data from different sources a facility was
added for loading gradient information from text files.
 Unused tabs are hidden.
 Opening of the input data settings window is much faster.
 Parallel processing changed so that one processor remains free.
 NaNs are returned for masked pixels, when parametric mapping fails, or when the
result value is beyond the restriction range.

Data Formats  DICOM: Added support to handle and save padding values (values outside actual
imaged area). NOTE: this affects the precision of scaling floating point data to 16-
bit short representation and may change region statistics when short data
representation is used during processing or as a final result.
 DICOM: Support for reading and saving DWI MRI gradient information.
 DICOM: Special cases extended by protocol name.
 Reader of Philips PAR/REC research file format implemented for 4D flow images.
 JPEG: Added support to read image resolution (JFIF APP0 x, y density and units)
for defining the image pixel size.
 New loader "Generated" which allows creating empty, chessboard and fractal
 PMOD Software Release Notes 9

image series. Such synthetic data may be useful for testing.

Zürich, October 26, 2015

10 PMOD Software Release Notes

Maintenance Builds of Release 3.6

Build 12  VOI: A slight bug fixed for the "Move to Max/Min" function.
March 4, 2016  Report saving: On Windows systems it was not possible to save multiple times
from the same dialog window.

Build 11  Fusion initialization improved. Important for users working with the last Inveon
Jan. 7, 2016 version and using the PET/CT option.

Build 10  Fix of report saving. After saving to a DICOM file the text input areas were
Oct. 21, 2015 inactive.
 Java and WIBU drivers updated for compatibility with Windows 10 (Java SE 8
Update 60, WIBU Version 6.32).
 Compatibility update of R console for El Capitan MacOSX.
 DICOM: Fix for reading multiphase NM files.
 DICOM: Fix for saving image data with slices filled with NaNs to Enhanced
Objects.
 DICOM: Added handling of slices direction for Siemens Mosaic files.

Build 9  VOI: "Hypoxia index" introduced as an additional statistic (defined as the

Aug. 31, 2015 percentage of pixels in a VOI which are above a threshold specified by the
operator).
 PXMOD: Revision of iterative 2-tissue compartment model: Use of the parameter
settings on the pre-processing tab in pixel-wise fitting.
 R: Time mid used for TACs loaded form statistics files when sent to R-Console.

Build 8  PKIN: Bolus/Infusion model will always use Powell optimization, as Marquardt
July 24, 2015 didn't work reliably.
 PFUS: Fixed problem with application of manual transformations in fusion batch
mode processing.
 PXMOD: Fix to support the translation table in the C14-Autoradiography models.
 Histogram external tool: Fix of number of bars calculated from width in VOI min /
max range.
 PSAMPLE: Resampling is restricted to return positive values.
 DICOM: Incoming folder was sometimes deleted after importing data.
 MicroPET: Improved handling of dynamic gated images.
 Nifti: Support extended to allow selection of the source of the image orientation:
qform or sform.

Build 7  PKIN: The activation time in the LSRTM model can now be fitted.
June 2, 2015  PFUS: Support for transformations paired with images in batch mode.
 PFUS: Protocols of Fuse It now also include the data averaging range.
 PNEURO: Problems with using small animal atlases in protocols fixed.
 Batch pipeline: New result naming option for excluding tool names.
 Batch pipeline: Bug fixed when only non-image results were configured for saving.
 Segmentation: k-means clustering added (again) to the general segmentation tool.
 PMOD Software Release Notes 11

 VOI: Transformation improved for VOIs saved on images with smaller bounding
box than current image.
 Peak VOI: Fixed problem which occurred if the initial VOI was defined in X or Y
direction.
 Atlas creation: When creating an atlas from a VOI set, a PET and an MR template
can now be specified.
 DICOM: Some acquisition parameters (e.g. kVp) that are stored at the image slice
level but have same value within the whole volume are now copied to the
coregistered image.
 P3D: Saving of last segmentation result as an image fixed.
 PSAMPLE: After the correction TAC was closed, no other TAC could be loaded.
 ITK: Unsuccessful filter loading had blocked the ATL and online versions.

Build 6  PNEURO: Possibility to use already normalized images for creating a Brain Norm
April 15, 2015 added to the Norm Editor.
 PNEURO: Improved handling of user-defined atlases without probability map
definition.
 PNEURO: Option in batch mode to create multiple protocols for the MR-only
situation.
 R Console: Restriction for aggregate size removed, and image size limit extended
to 1500x1500 per slice.
 R Console: "Linear Model" script renamed to "rm-Anova/Manova" for clarity;
report plots performance improved.
 R Console: configuration of printout font added.
 PVIEW: TACs sent to PKIN now handle NaNs in the same way as Statistics.
 VOI: Intersection when using a dynamic mask file corrected. The first mask frame
was always used.
 VOI: In pipeline operation statistics calculation relative to merged VOIs was fixed.
 Database interface: Study date filter added.
 PCARD: The actual units (eg. kBq/cc, SUV) of the image data are used to display
curves, tables and polar plots.
 Distance measurement: Fixed in zoomed fusion display.
 Data aggregation: Series description column added to the component selection
interface.

Build 5  LSRTM model: Fixes in PKIN and PXMOD to accommodate series with gaps
Feb. 23, 2015 between acquisitions.
 PKIN: Removed the filtering of very small stdvs in Monte Carlo simulations.
 PNEURO: Outlining fixed in the case of PET result space with transformation
loaded from file.
 PFUS/PFUSEIT: Batch mode save fix for the combination of Database input format
and different output format.
 PGEM: Graph synchronized with tree to select model elements.
 R Console: generator for patient IDs added to simplify anonymization.
 New option to reslice loaded series to common space and average at the same
12 PMOD Software Release Notes

time.
 DICOM: Fix for reading RTSS structures containing empty contours.
 Normalization tool: Worked only when scaling (normalization) had been enabled.
 Image history for motion correction fixed. The selected frame was always reported
0.
 Scientific screen capture improved for switched series.
 Saving of NaN values added for float DICOM and Database formats.
 Cardiac MR module activated again.

Build 4  Installation of upgrades improved to avoid database overwriting.

Jan. 13, 2015  Additional status icon indicating the availability of a new version build.
 PKIN: Sensitivity functions were calculated in "1/1" units rather than the indicated
"%".
 PKIN: The standard error of the slope was incorrectly scaled for the Logan
Reference and RE-GP models.
 PNEURO: A white-matter VOI is also generated for PET-only cases.
 PNEURO/Mapping: VOIs used in parametric mapping can be created by VOI
merging.
 PNEURO/Mapping: A mask can be created from the brain matter segments or
from a VOI selection.
 Fuse It: Coupled cursor added to "Comparison" page.
 Fuse It: Facility added for paring inputs and references which are loaded as
separate lists.
 Fusion: Problem fixed when loading motion correction transform without a
reference.
 PXMOD: Fix for PBnd_MRTM0 in 6 Calc Method.
 Rat and mouse templates were converted to a right-handed coordinate system.
 R: Repeated measures ANOVA added to LM analysis.
 R: Fixed problem with plots for Mac and Linux.
 R: Reconnection to R server more robust.
 The “GM & WM & CSF Probability” external tool was renamed to “MRI
Probability and Inhomogeneity". It allows saving of the denoised and
inhomogeneity corrected MR images.
 PGEM: 3D mesh generation possible without running an actual simulation.
 PGEM: User interface for CFD case creation and the handling of cases improved.
 PGEM: Update of the heartatlas structures.
 Dual-monitor option removed due to unpredictable results.

Build 3  VOI: Fixed loading of RT Structure Sets without references to DICOM images.
Nov. 24, 2014  VOI: Fixed average calculation for the last VOI in the list.
 PNEURO: Saving of all results in batch mode fixed.
 Fuse It: Markers matching improved when repeated markers adjustments are
necessary.
 PMOD Software Release Notes 13

 PKIN: Sometimes not all regions were listed in the "View Par" window and NaNs
were saved instead of the correct parameter values.
 Gaussian filter in time domain added, with circular option (also for Median filter).
 Configuration improvements for the ATL license.

Build 2  R Console: Bartlett and Kruskal-Wallis results accumulated in tables; online helps
Nov. 4, 2014 added; improved descriptions and error handling; pm.base package version
update; pixel dump script fix; variables shown after workspace loading; clean
option for workspace loading.
 "View aggregated" window unified to support combination with external data and
transfer R Console in all places.
 Peak VOI: Options to use a background threshold and require a minimal included
fraction of the sphere volume inside the original VOI.
 VOI atlas normalize function: uses the corresponding species presets directly.
 PBAS segmentation: k-means clustering removed.
 PSEG: New k-means clustering options whether to work on the dynamic data,
each frame separately, or on the average.
 PSEG: Option to outline all segments of the selected frame as VOIs.
 Save to buffer option added to the "Save all" function of PFUS, PNEURO, PSEG.
 Cropping box in PFUS, PNEURO, PSEG: edge sizes can numerically be defined.
 PFUS: Unified options mm/pixel for sampling and smoothing in all matching
methods.
 P3D: Close all button added; online help introduced.
 PMOD can be restarted directly after a configuration change.
 License server: new "-lic[<pattern>]" commandline option for starting multiple
license servers in a common installation, e.g.
java -Xmx2G -jar pmtsvr.jar 5000 -ls -lic[1324]
java -Xmx2G -jar pmtsvr.jar 5001 -ls -lic[427]
These licenses can then be referred to in the client scripts with the
-lsn[<PORT_NO>.<OPTIONAL_LICENSE_NO>@<IP_ADDRESS>] option.

Build 1 Initial upload of 3.6 version.

Oct. 17, 2014
14 PMOD Software Release Notes

Product Release 3.6

The 3.6 product release brings major functional improvements for pipeline processing which allows
constructing comprehensive analysis procedures, a completely novel population statistics via the R
console, and an additional tool (PFUSEIT) for image fusion with redesigned workflow and new features.
Also added is a new tool (PGEM) for the development of geometric models. Additionally, many
improvements were implemented for the various tools and the platform, whereby the list below only
highlights the major points.

Features

General Batch Pipeline Processing: Substantial extensions of functionality such as

 Brain VOIs can be generated on anatomic images and applied to functional images
for TAC generation.
 Generated TACs can be submitted for kinetic modeling.
 Quality-control options added: image viewing, VOI editing, JPEG image saving.
 Results can directly be aggregated for population statistics.
 Various external tools optimized for use with batch pipeline: CoRegistration and
motion correction with interpolation choice; and VOI statistics with spatial
transformation, morphological operations, and relative to reference region; VOI
based PVC simplified; Interpolation tool can apply transformation; Background
removal tool; Segmentation tool supports VOI outlining.

VOIs:

 New inclusion criteria for contour VOIs: 1) All pixels with a fractional part covered
by the VOI are included, and the average is weighted according to the included
pixel area. 2) Using pixels with 50% or 100% area included, with unweighted
averaging.
 SUVpeak: Generation of explicit sphere VOIs within an enclosing VOI. The
positioning options are centering on the maximal pixel, or to maximize the average
enclosed in the sphere.
 Localization of a number of hottest pixels within a VOI.
 Morphological operations (erosion, dilation etc.) of a whole group of VOIs, for
instance to shrink automatically generated VOIs by 1 pixel.
 Calculations of VOI pixel value histograms, which can be analyzed in R (skewness,
kurtosis).
 Use of predefined VOI name lists.
 Tool for reducing the number of contour vertices.
 Eraser working on all active VOIs when the Group tab is selected.

Miscellaneous:

 Java Version 8 is bundled with the distribution, now also for Mac.
 Aggregation improved, particularly for group analysis. Group name and condition
can be specified.
 Animated GIF option for saving movies added.
 PMOD Software Release Notes 15

 Yearly filter added to improve components listing speed. Important for large
databases.
 DB components loading speed optimization from large databases. Particularly
relevant for PXMOD and PNEURO.
 Automatic crop box calculation added based on subject end modality (PFUS,
PALZ, PNEURO, PSEG).
 Spline interpolation introduced for reslicing (PFUS, PALZ).

Changed:

 The Automatic Brain VOIs external tool is based on image matching technology
and is therefore now bundled with the PFUS option.

PFUSEIT The new "Fuse It" tool guides the user step-by-step from the input images to the
registered and post-processed results. Common tasks can be achieved in only a few
straightforward steps, whereas complications are handled separately by additional
steps. The new tool is launched as a companion tool to the 3.6 version of the proven
Fusion tool, for allowing users familiar with the old interface to continue their work as-
is. This coexistence will be supported for some future versions, but new developments
will mainly be included in the "Fuse It" tool.

Novelties in "Fuse It":

 generation of rotating MIP images fused from up to three sources, including

animation over time;
 explicit use of species information (HUMAN, RAT, MOUSE) for proper matching
presets;
 parallel viewing of up to 6 fused renderings;
 whole-body layout for improved display of non-cubic data;
 reference can be reoriented before the matching;
 a "Run all" operation mode which applies the configured methods to data selected
in the database;
 support of overlapping criteria (Dice, Jaccard, volume difference, signed volume
difference, specificity, Sensitivity)
 transformation of markers after matching;
 support for the normalization of CT brain images using a conversion of the HU
values and template images from an elderly population (Clinical Toolbox, Chris
Rorden).
16 PMOD Software Release Notes

 Population analysis implemented based methodology developed by Prof. K.

R statistics Herholz
Console
 Statistical analysis of study data with numerous regional outcome values, which
raises the problem of multiple comparisons.
 Streamlined MANOVA and Linear Mixed Effects (LME) analysis workflows.
 Scenarios covered include the comparison of groups, the interaction with regional
effects, and the handling of covariates, such as age and gender.
 Additional tests: Kruskal-Wallis, Variance analysis using the Bartlett test.
 Import of data from SPSS, SAS, Systat, Stata, CSV and conversion to aggregates.
 Improvements for pixel-dump analysis.
 Own operating-system independent package pm.base.tar.gz added containing the
scripts.
 Multiple user interface improvements.

PKIN New:

 Fitting mode which sequentially shortens the data segment used.

 The model history supports multiple new options. The change of a parameter
across different fits (eg. shortening) can be visualized as a plot.
 The configuration of all models (tissue, blood) can be saved in a single file.
 The Sigmoid, Watabe and Hill functions can also be used as plasma fraction
functions.
 Sigmoid parent fraction function added which was described for [11C]-PBR28 by
Owen et al.
 Two-tissue compartment model developed by Rizzo et al. for the analysis of [11C]-
PBR28 uptake in the human brain.
 Alpert’s Linearized Simplified Reference Tissue Model (LSRTM) for noninvasive
detection of neuromodulatory changes in specific neurotransmitter systems added.

Improved:

 Handling of fitting failures: Regions are not shown in the parameter overview and
not saved in the kmPar file. Failures in the reference region are not reported.
 Monte Carlo simulations now use an independent seed for each data sample.

Changed:

 Runs test: The restriction of >8 runs and >16 samples was removed, and a
correction for small sample sizes (N<50) was introduced.
 Inclusion of the residual weighting scheme into the tissue model configuration file
(.kmModel).
 PMOD Software Release Notes 17

PNEURO  Animal brain atlases (mouse, rat, monkey) also supported.

 Completely revised batch mode which allows defining a processing scheme for a
whole list of input data. In this way processing variants can easily be applied to
large data samples.
 Automatic image cropping mode added so that the entire processing can run
without user interaction.
 Alternative normalization of MR images which uses the template images directly,
rather than the tissue probability maps.
 A Hammers atlas variant with 1mm resolution is available which provides more
accurate VOIs in the MR space.
 VOIs resulting from parcellation can also be obtained in the atlas space.
 Parametric mapping can directly be performed in PNEURO, if the PXMOD tool is
licensed. The VOIs can be applied to the maps, and the maps can also be used in
norm comparisons.

PSEG  Automatic species recognition added based on the image volume.

 The anatomic images (MR, CT) are directly resampled to the functional images.
 K-means clustering added as an alternative method for generating cluster maps.

P3D  JOGL is used as 3D engine allowing 3D on Mac with Java 1.8.

 New page for the generation of high-quality rotating MIPs. Up to 3 images may be
fused. For dynamic scans, the temporal evolution of the images can be included in
the rotations.
 A scene consisting of surface objects can be saved to an STL file. The object tree is
reconstructed after loading the STL
 Support for the more compact binary STL format.
 3D properties can be set on the Segment page before rendering.

PXMOD  Alpert’s Linearized Simplified Reference Tissue Model (LSRTM) for noninvasive
detection of neuromodulatory changes in specific neurotransmitter systems
 Image definition and loading are now done in a single step.
 Several user interface optimizations.

PGEM This new tool leverages the PMOD platform for supporting various types of
simulations. A model builder allows for the construction of anatomic structures from
VOIs, resulting in a geometric model. Such models can be enriched by multimedia
annotations for creating educational 3D-scenes, and complemented by tissue
properties. Based on the model construct, phantom images can easily be generated
which represent a well-defined input for external simulators of image acquisition
instruments or physiology, e.g., OpenFOAM® or Fluent®. An alternative output
constitutes atlases which can be employed for automatic VOI generation.

Data Formats  Improved handling of floating point image data with NaN values (interpolation
and smoothing).
 Fixed problem with reading patient and acquisition information from de-identified
files with no de-identification method element (0012,0063) included.
 Information on image de-identification can be shown in the series info dialog, if
present in the DICOM file.
18 PMOD Software Release Notes

 Corrected encoding of HU for DICOM enhanced images.

 DICOM Incoming folder support for MicroPET and Interfile. Device specific
folders with an initial transformation.

Zürich, October 17, 2014

 PMOD Software Release Notes 19

Maintenance Builds of Release 3.5

Build 10  Local R installation improvements: No administration privileges required for
Oct. 16, 2014 package installation.
 PKIN: Displayed weighed residuals were wrong: division by stdv instead of
stdv^2.
 PKIN: In Monte Carlo stdvs<1e-4 had been masked, which is inconvenient for rate
constants with small values.

Build 9  PNEURO: Fixes for reducing RAM consumption during batch operation.
Aug. 7, 2014  PNEURO, Maximum Probability Method: Fix for a situation when splitting of the
hemispheres fails. In this case white matter is not separated into left and right
parts.
 PNEURO: Crop box is saved in protocols without explicit cropping during
protocol preparation.
 PKIN: For the blood-related interpolation models calculated weights did not
include the decay effect.
 R Console: Statistics calculated using atlas VOIs could not directly be transferred
to the R console.

Build 8  Java compilation error fixed which manifested itself when loading a
June 4, 2014 transformation.
 PFUS: Fix of a synchronization problem in triple fusion.
 PXMOD: The k2 map of the SRTM2 model had been incorrect.
 PKIN: The correction of the AIC for small sample sizes had been inactive.
 PKIN: Default of third exponential half-time slightly adjusted for plasma fractions.

Build 7  Java Runtime Environment updated to Java SE 7u55 for security and compatibility
May 17, 2014 reasons (stability problems on Win8.1).
 R: Problem fixed with installing additional packages.
 R: Data extraction from aggregates improved.
 VOI: Interactive 3D iso-contouring used wrong seed coordinate in the fusion
display.
 PNEURO: The statistics were not properly updated when using the "Relative to"
mode, in case the image was changed.
 PNEURO/Compare to Norm: When importing a Norm, the VOIs defined for
results averaging were not properly handled.
 PFUS: Saving the inverse of a manual transformation was fixed.
 PFUS: The 3D scatter plot had only rendered the samples for one VOI.
 Scaling tool: A facility was added to convert CT values to a value range useful for
normalizing the image to the Clinical Toolbox template
(http://www.mccauslandcenter.sc.edu/CRNL/clinical-toolbox).
 DICOM: The image presentation information was not properly used when
selecting a frame subset at loading.
 Aggregation: When combining aggregates with external data, only the "Patient
Name" key worked, not the "Patient ID".
20 PMOD Software Release Notes

 MINC 1 format: Images stored in coronal and sagittal orientation are now also
supported.

Build 6  PKIN: An inappropriate interpolation method had been shown when using the
March 11, 2014 plasma fraction.
 PKIN: It had not been possible to configure certain models.
 PKIN: Models used in loaded data and not configured are automatically added.
 PKIN: Improved refresh at the end of batch mode.
 DICOM: Improvement of the extended association negotiation and the
interoperability with the Mediso DICOM server.
 PNEURO: A problem with parcellation in the absence of properties has been
corrected.
 PNEURO, PSEG: In the case of overlap (which is inappropriate) the affected VOIs
are not added to the statistics and a warning message is shown.
 R-Console: A problem with SUV units was fixed, and VOI names now may contain
the "%" character.
 Network license selection: If a customer has multiple license servers, the proper
license server can be specified as a PMOD client command line option by:
-lsn[<PORT_NO>.<OPTIONAL_LICENSE_NO>@<IP_ADDRESS>]
 Transaction server configuration: The storage path is verified to ensure that data
can be stored.

Build 5  PKIN: Fix of the model list shown for plasma activity loaded from file.
Jan 27, 2014  PKIN: Sum of 3 exponentials better initializes the begin time, namely to the signal
maximum.
 PNEURO: Option to selectively enable/disable sulci deformation for both the
Maximum Probability and the Parcellation method (default = off). In parcellation it
had previously always been applied.
 PNEURO: Progress information improved.
 PNEURO: 3D rendering problem fixed.
 PFUS: Load protocol better supports data format changing.
 Sizing of the curve control area improved.

Build 4  R console improvements and fixes: Plots did not work on Windows systems.
Jan 12, 2014  Pipe processing: Error handling improved so that errors terminate processing.
 SUV external tool in pipe processing returns an error for zero injected activity in
the data.
 Data association functionality extended so that external segments can be used in
the PVC external tool. In this case the MR segmentation step is omitted.
 The external segmentation tool applies the same colortable as the processed data.
 ATL database export: Speed (factor 2.5) and stability improvements.
 PKIN: Curve zooming extended by a factor of 100.
 PMOD Software Release Notes 21

 PNEURO/Compare to Norm: Option added to limit z-score clusters by the

minimal number of included pixels.

Build 3  PNEURO, Norm Comparison: Cluster analysis with a specified maximal number
Dec. 22, 2013 of clusters.
 PNEURO, Maximum Probability: Sulci bottom detection available as an additional
segmentation option. It adjusts the VOIs such that they end in the sulci bottoms.
 PNEURO, Maximum Probability: Support for user-defined atlases, which may also
define animal brain VOIs (monkey, rat, mouse).
 PKIN: Display layout showing the curves from all regions revised. All TACs,
targets or model curves can now be shown.
 R: Identity line option added to the scatter plot.
 R: Support for box plots showing multiple variables.
 R: Verification of packages at start time.
 R: Data reduction procedure implemented for pixel-dump and image data, to
increase loading speed.
 PXMOD: If mask and VOIs are not manually saved when proceeding, a dialog
window appears and simplifies saving.
 PXMOD: VOIs used in preprocessing are initially switched off on the parametric
maps.
 Mapping of pixels defined in scatter plots back to the image space supported in the
"Segmentation" procedures.
 Arbitrary ROI definition in scatter plots via conversion into an image and usage of
the standard VOI functionality.
 Improved synchronization of the SUV units shown in the data inspector curve
display.
 DICOM Loading: Handling of Philips ADNI images with wrong high bit value.
 DICOM Saving: Fix for using the proper output SOP selection.
 Analyze: Improved handling of the origin for files stored in little endian.
 Display: Inspector TAC updated also when triangulating via the MIP image.

Build 2 PNEURO: IMPORTANT - it is necessary to replace the parcellation resources for

Nov. 11, 2013 taking advantage of the improvements. This is most easily done by removing the
directory Pmod3.5/resources/parcellation. When restarting and calling PNEURO, an
appropriate download link will be shown.

 PNEURO, Maximum-Probability method: Partial-volume correction improved.

The VOI parts removed by gray-matter thresholding are considered as
complementary VOIs and used for PVC.
 PNEURO, Maximum-Probability method: Ventricles not affected by masking with
the segments map.
 PNEURO, Maximum-Probability method: White-matter VOIs are initially hidden.
 VOI: Smoothing option introduced for the iso-contouring tool.
 R: Improvements for sending pixel dump results to R. Preview, and support for
multiple data files.
22 PMOD Software Release Notes

 R: Revision of the scatter plot solution for better visualization.

 Fusion: The separate color table used for fusion can be inverted separately.
 External VOI-based PVC tool: The Hammers N30R83 atlas can also be selected, if
PNEURO is licensed.

Build 1 Initial upload of 3.5 version.

Oct. 22, 2013
 PMOD Software Release Notes 23

Product Release 3.5

The 3.5 product release brings major improvements for the PNEURO and PKIN tools, as well as for the R
statistics interface. Additionally, many improvements were implemented for the various tools and the
platform, whereby the list below only highlights the major points.

Features

General VOIs:

 New VOI statistics: surface estimation, maximum diameter, sphericity and area
under curve.
 Use of B-Splines between vertices to create smooth contours.
 SUVR calculation easily possible in statistics panel.
 Multiple user interface improvements of statistics panel: VOI merging, sorting,
show only selected information.
 Improvements of VOI tree handling.
 VOI/ROI/Contour toolbars reorganized.

Miscellaneous:

 Flexible marker use: set markers by coordinates specification; distance map for a
set of markers; sum of distances between two sets of markers; intensity profile
along a set of markers; spatial transformation of markers.
 Aggregation: highlighting of common parameters, adding of covariates to the
data, control over the aggregation order.
 Database: Replication facility for migrating the database information to a new
database without actually moving the data; response accelerated; facility for
adding project/diagnosis/comment when saving to database; C_STORE option for
data export; "last month" and "last year" filter added.
 Pipe processing and external tools improvements in: SUV conversion; histogram
calculation; median filter in time domain; pipe organization and results saving.
 Interference of automatic reorientation and macros solved in several tools.
 Linear regression added to 2D scatter plots.
24 PMOD Software Release Notes

The PMOD R console provides an interface to the R package and leverages the entire R
R statistics
Console functionality including the statistical analysis of PMOD results from populations. The
methods can be applied to the outcome of VOI statistics, regional kinetic modeling,
cardiac perfusion quantification and the PALZ analysis.

Standard analysis types are directly supported via the graphical user interface. They
can be as simple as a performing scatter plots, but range to more complicated
techniques such as ANOVA, test-retest analysis or Bland-Altman comparison.

Beyond using the graphical interface for invoking R functionality, users can also
develop their own analysis scripts in a command window interface. In this situation,
the PMOD R console serves as a prototyping interface which allows to enter R code,
execute it, inspect the result, and improve the code.

Compared to version 3.4 the whole functionality, including data preparation, was
revised and extended.

PKIN New:

 Multi-model fitting: Support for fitting data with multiple models at once.
 Filtering options for tailoring the model list to the actual data (e.g. models
with/without blood data, reversible/irreversible configurations, etc).
 Saving of the model fitting history in the km file such that prior configurations can
easily be recalled.
 New tissue model: 2-tissue compartment model with k5 efflux.
 New tissue model: 3 sequential tissues described for FDG in skeletal muscle.
 New tissue model: Multi-linear approach for estimating the influx of irreversible
tracers (MLAIR).
 New tissue model: Utility for calculating OLINDA-ready residence times in
dosimetry studies.
 New blood model: Gamma function peak plus two exponentials.
 New plasma fraction: linear plasma/whole-blood ratio.
 New composite data format for importing all data parts at once.
 New curve tools: Decay correction, decay un-correction, volume edition,
acquisition times trimming.

Improved:

 Batch mode: Support for composite data format and multi-model fitting.
 The organization of the blood data has been unified for all input curves of models
with more than only a single input curve.

Changed:

 Modified gamma functions 1 and 2 deprecated.

 Model for cardiac water PET with geometrical correction removed.

PNEURO New:

 Batch mode support for brain VOI generation.

 PMOD Software Release Notes 25

 The landmarks required for the brain parcellation are now automatically
generated, making this method batch-able and easier to use.
 Parcellation now also estimates Hippocampus and Amygdala from the knowledge
base.
 Parcellation performs a sulci optimization with the cortical VOIs.
 Support for the AAL-Merged atlas as well as user-defined atlases in the MNI
space.
 Introduction of the tree structure for the AAL atlases.
 Addition of regions to the AAL atlas for making it more comparable to the N30R83
atlas.

Improved:

 Harmonization of the workflow and the resulting VOIs across the two brain VOI
approaches.
 Brain norm editor better streamlined and the probability map normalization
added.
 Additional parameters made available for segmentation and matching.

Changed:

 New knowledge base for the parcellation, now including 26 rather than 14 normal
subjects (all non-smokers; female: 3, left-handed:1, age: 34±12, min 19, max 29).

PSEG  Species selection: HUMAN WB and HUMAN BRAIN added.

 List of cropping sizes adjusted to species selection.
 Instead of overwriting existing VOIs with the same name, structures can now also
be appended.
 If an anatomical image is loaded, it is pre-selected for fusion with the segments.
 Hot region growing added to the default VOI tools.

PCARDP New:

 Facility to replace the LV curve by an externally created curve (e.g. obtained with
an online blood sampler).
 New crop box sizes suitable for rodents.
 Simplified data loading by associating rest and stress scans in database.

Improved:

 Behavior of data loading for creating factor images for water bolus studies.

Changed:

 2-tissue compartment model for Rb: Vd removed corresponding to differential

equation system.
26 PMOD Software Release Notes

P3D New:

 Smoothing added to VOI rendering protocols.

 Markers defined in images are rendered when transferring the images to P3D.

Improved:

 Functionality of Segmentation page.

 Tree allows multiple nodes with the same name.

PXMOD  Transfer of pixel-TACs to PKIN optimized.

 Improvements of workflow.

PALZ  Crop box added.

PFUS  Additional brain normalization procedure using tissue probability map

information.
 Facility to map points localized in a 2D scatter plot ROI back to the image space.
 Scatter plot analysis tool.
 Support for a prefix to the original file name when saving multiple matched series.

Data Formats  Bruker Paravision MR loader added.

 MINC 1 loader added.
 DICOM: Preview facility for the DICOM Special Cases; export/import of nodes list;
various improvements for different devices.

Zürich, Oct. 18, 2013

 PMOD Software Release Notes 27

Maintenance Builds of Release 3.4

Build 9  Java Runtime Environment updated to Java SE 7u55 for security and compatibility
May 17, 2014 reasons (stability problems on Win8.1).
 PNEURO: Parcellation could be started even when both deep nuclei and cortex
parcellation were switched off.
 PNEURO: Fixed problem of loading gray matter template in parcellation in case of
previous loading of dynamic series by Autodetect.
 PKIN: Incorrect times had been used when switching from Logan to the B/I model.
 ATL version: Incoming folder processing could close DICOM Server.

Build 8  PKIN/PXMOD, Patlak plot: The plasma activity had only been integrated from the
Sept. 23, 2013 time of the first sample. Corrected to add area of linearly integrated blood activity
assumed zero at time 0.
 PKIN/PXMOD, Patlak Reference Plot: Independent of the t* setting, the whole data
segment had been used for the linear regression.
 PNEURO: Partial-volume correction had not considered the parts of the activity
outside the gray-matter intersected VOIs. Complementary VOIs are now included
in the correction.
 VOI: Loading with transformation could result in truncated VOIs when they were
outside the field-of-view.
 VOI: Statistics within a range did not work properly when invokeded repeatedly.
 VOI: Intersection of dynamic VOIs was not correct for frames beyond the first one.
 VOI: Compatibility option for statistics saved with the 3.3 version replacing the
space character by "_" in descriptions.
 DICOM: Support for fixed color scale in the generation of SC DICOM output.

Build 7  P3D: Improvement of protocols including VOI renderings.

July 12, 2013  PNEURO: Initial 3D rendering limited to VOIs, but the skull-stripped MR is also
made available for rendering.
 Fix for a VOI undo problem in PNEURO and PSEG.
 Pipe processing: path definitions were not working for data other than DICOM or
database files.
 PCARDP: Protocols for ammonia didn't store the flag for calculation of the MBF
maps.
 PCARDP: Stress/rest is now detected in the series description when performing
the factor analysis for water PET studies.
 ECAT: Improved support of the origin coordinates.
 Save all: better handling of the settings across the saved files.
28 PMOD Software Release Notes

Build 6 PSEG Tool Released: New tool for the semi-automatic segmentation of dynamic
April 22, 2013 rodent PET series is available. Please refer to the product description on
www.pmod.com for details.

 PNEURO: Support added for using the MR segments calculated in a prior

PNEURO session. They can be loaded together with their transformation to the
atlas space.
 PNEURO: Improvement of the parcellation result by removing spurious isolated
pixels.
 PCARD: The factor images generated for water studies can be cropped before
short-axis reorientation.
 PCARD: Protocols include recalculation and cropping of factor images.
 PFUS: Fix for an initial slice offset due to differing slice thicknesses of the reference
and the input series.
 PVIEW: Fix of a problem in the Split slices and Split frames procedures.
 Save All function: Revised interface fixing a bug in propagation of changes.
 Series description added to Data Inspector title bar.
 Option to switch off automatic checking of available updates.
 Fixed problem when saving reports with multiple pages as DICOM SC objects.

Build 5  PNEURO: The VOIs are saved with the protocol definition to preserve manual
March 7, 2013 edits.
 PNEURO: Facility for saving all intermediate results of interest at once with a save
all button in the lateral taskbar.
 PKIN: Handling of time-overlaps occurring due to erroneous DICOM time
encodings.
 R statistics: Multiple functional improvements.
 Scaling tool: new options (divide by VOI average, scale to 1 or 255 max).
 VOI: Masking inside VOI using its own VOI average.
 DICOM: Improved handling of PET frame reference time values. Automatic
calculation of frame start and end times for PET images referring the time of
average activity.
 External Histogram tool: extended with "In VOI" option.
 PCARDP: Zero time setting had not been applied when using factor analysis.
 Transaction server: improvements in starting and status reporting.
 Default configuration: Raw and Query data loaders added.
 Distribution: Java updated to JRE 1.7.0_17. WIBU Key driver files updated to
6.11.1057.500.

Build 4  PNEURO: Cortical VOIs are created using the approach of the Maximum
Jan. 14, 2013 Probability tool.
 PNEURO: FDG or other PET images with anatomical information can be used for
determining the normalization transform, replacing the role of the MRI.
 PNEURO: Organization of the Hammers VOIs in a hierarchical tree. This also
allows simplified merging functions.
 PMOD Software Release Notes 29

 PNEURO: Facility to save the different transformations between the spaces.

 PNEURO: The VOI volume is calculated instead of the value average in the case of
MR-only analyses.
 PNEURO: Partial-volume correction now also considered the complementary
white-matter parts of masked VOIs. Improved interface for adding scanners.
 PNEURO: Protocols can be used for loading configurations without starting
processing.
 PNEURO: Fix of unit support in protocols.
 PNEURO: Volume-weighted averaging of curves added on Statistics page.
 PCARDP: Improvements of the factor image reorientation for water data.
 PCARDP: Simplified loading from the side bar of dynamic and transmission
images for factor analysis.
 PFUS: The data of scatter plots can be saved as statistics from the context menu.
 PFUS: RGB images can be fused with monochrome images.
 PKIN: Regions containing "cerebellum" or "reference" in the name are now pre-
selected for the reference region after data import.
 PKIN: Fix of the Ito plot results. The result parameters were interchanged (Vt <->
Vnd, K1<->K1') and BPnd not calculated.
 PKIN: Dedicated filters for loading data didn't work.
 VOI: Multiple VOI sets of an image can be converted into mask files.
 VOI: Masking by average value in VOI added.

Build 3  PXMOD: The program could freeze for some model configurations when running
Nov. 24, 2012 all processing steps.
 Acceptance tests fixed for the ATL version.
 PNEURO: Fix in the calculation of the lateral frontal horn thickness.
 PNEURO: Improvements when switching between workflows.
 PNEURO: Denoising option added to Maximum Probability solution.
 PCARDM: Improved compatibility with prior protocols.

Build 2 CAUTION: Due to Java-related errors users are strongly recommended migrating
Nov. 8, 2012 from Build 1 to Build 2.

 Java: A severe bug was detected in the Oracle JRE 1.7.0_07 distributed with Build
1 which caused unpredictable numerical errors. The PMOD installation packages
were updated with JRE 1.7.0_09.
 PNEURO: New normalization procedure for T1-MR images which dramatically
improves the quality of the VOIs in the Maximum Probability module.
 PNEURO: Time-weighted average statistics added for dynamic PET scans.
 PKIN: Tissue model curves and compartment model curves shown in HD.
 VOI statistics aggregation: Improvements and fix in handling of old format
statistics.
 Cardiac PET: List of recognized ammonia strings extended.
 Cardiac PET: Fix for handling a problem with manually shifted EPI/ENDO
30 PMOD Software Release Notes

contours.
 Cardiac PET: The excess ENDO TAC was removed.
 Cardiac PET: Static input creates polar plot with average values in AHA sectors
instead of the individual samples.
 R statistics console: More plots added (histogram,scatter plot, box plot, density
plot).
 DICOM: Fixed problem with saving private slices orientation and position
elements for NM objects with more than 1365 frames when explicit transfer syntax
is used.

Build 1 Initial upload of 3.4 version.

Oct. 16, 2012
 PMOD Software Release Notes 31

Product Release 3.4

The 3.4 product release includes a completely revised and functionally extended tool for the analysis of
human brain images, as well as a new module for the quantification of cardiac MRI images. Further, in
order support the users with their statistics analysis, an interface was developed to the "R" statistics server.

Features

PNEURO The former PBRAINDB tool has been completely revised and extended. In addition to
- EXTENDED the normal brain database functionality two modules were added for the automatic
generation of human brain VOIs, one using the Hammers N30R83 maximum
probability atlas, the other parcellating T1-MR images. See product brochure for more
details.

PCARDM A new tool for cardiac MR was jointly developed with the CMR research group of ETH
- NEW Zurich, Switzerland. Using PCARDM, researchers in the field of CMR may apply the
state-of-the art perfusion quantification approaches to their data and compare them
with the standard qualitative outcome or an external gold standard. For version 3.4,
the cardiac MR tool is bundled with the cardiac PET tool. See product brochure for
more details.

General A lot of effort was devoted for assembling numerical PMOD results and connecting
PMOD with the "R" open-source statistics environment (www.r-project.org). The idea
is that the user can easily aggregate results for comparing methods or populations and
analyze them in "R". A variety of numerical results can be analyzed in this manner like
VOI statistics and modeling parameters.

New:

 The PMOD distribution includes the latest Java 7 version.

 R-console: facility for connecting to "R" servers, transfer data, send commands for
analyzing the data, retrieve the results and visualize them.
 Direct saving of aggregates as an Excel file.
 The "PMOD Version" area in the ToolBox acts as a drop-box for files: When a file is
dropped (image file, protocol file, pipe, etc) the linked module starts.
 PSAMPLE and the R console can start automatically after user login.
 New association in the DB interface to support grouping of PET and MR segments
for partial-volume correction.

VOIs:

 New statistical measures added: median, area-under-curve (AUC), peak statistics

in sphere centered at the VOI maximum.
 Statistics can be calculated on all loaded images at once and the results shown on
tabbed pages.
 Interactive region growing and shrinking holding down the "Ctrl" key.
 Brush mode for creating VOIs and deleting from VOIs.
 Contour generation with the criterion of equality.
32 PMOD Software Release Notes

 New contour editing modes which disallow overlapping VOIs.

 VOI template for cynomolgus monkeys added.
 Intersection of VOI template with list contours.
 Statistics output window is not blocking any more.
 Saving of VOI statistics as DICOM Structured Report.

Improved:

 Pipe processing: Functionality extended for running multiple pipe definitions

subsequently. Macros and VOI statistics are now also supported in pipes. Partial-
volume corrections revised so that they can also be used in pipes.
 Time editing facility improved. Simplified shifting of time vectors and calculation
of start/end times from mid-times.
 New options in replace tool using the magnitude.
 Network license server supports multiple license files.
 License client can view state of licenses on the server.

PKIN New:

 Simplified fitting of the blood delay together with the tissue compartment model,
both for a single TAC as well as coupled TACs.
 Spectral analysis model added.
 Power-function damped three-exponential metabolite correction added (requested
for use with 11C-DASB). It handles the situation where the parent fraction starts at a
low value and then increases, before dropping.
 Blood delay parameter included in the model history.
 Visualization of min/max parameters in summary lists: min = green, max = red.
Columns with constant values are marked in blue.

Improved:

 Bug fix in the handling of a delayed input curve: There was an impact in cases in
which the inherent assumptions of the kinetic data are not met. Particularly, if the
input curve had significant contributions before time zero, and when the PET
frames were not started at time zero (=injection time).
 Simplified user interface for curve loading.
 Monte Carlo functionality for coupled fitting integrated into the Monte Carlo tab.
 Simplified selection of the regions to be coupled with long region lists.
 Units of curve plots revised.

PCARDP New:

 Definition of the endo- and epicardial boundaries as an alternative to the

centerline heart model definition.
 Cardiology-style report page showing the average uptake images of stress and rest
in the different orientations.
 Calculation of parametric MBF maps for ammonia using a basis function method.
 UCLA model for MBF quantification with ammonia.
 PMOD Software Release Notes 33

 Facility for cropping the images around the heart which is particularly useful
when the reconstructed images are not zoomed onto the heart.
 Visual support for optimizing time-averaging of the early and late uptake phases.
 Facility for saving the VOIs in the space of the MBF maps for comparison
purposes.
 Support for the aggregation of the result statistics.
 Vertical taskbar for data loading and results processing.
 Configuration option to reduce the number of visible VOI tools to the most
relevant ones.

Improved:

 Unified numerical results organization for dynamic and static studies.

 Protocols for water studies with factor analysis fixed.

P3D New:

 Completely new page for the object segmentation. The image space is larger, and
segment generation is easier and more flexible.
 When VOIs are directly submitted for 3D rendering from the viewing tool the user
is offered the choice between the rendering modes (surface, stripes).
 Texture color interpolation can be switched off, for instance for the visualization of
parcellated brain segments.
 Example protocol showing elements of the heart anatomy.

Improved:

 Better support for the STL (STereoLithography) format. Surface renderings can be
saved in STL and used for flow simulations (ANSYS Fluent) and for printing 3D
prototypes (Materialize MiniMagic). Loaded STL objects can be surface textured.
 Faster and smoother surface rendering of VOIs.
 Better control for the rendering of dynamic VOIs.
 More accurate visualization of the pixels to be included before the actual
segmentation.

PALZ New:

 Lateral taskbar for loading and closing of the image data.

 Facility for aggregating the statistics results of the PALZ analysis (only in non-
simplified mode).

PFUS New:

 Masking facilities for restricting the information used in matching and

normalization.
 Motion correction can be used in batch mode and in pipe processing.
 In batch mode and the interpolation tool the user can choose to use the resolution
of the input study, for instance in the case of a low-resolution reference.
34 PMOD Software Release Notes

PVIEW New:

 Stitching tool which automatically determines the overlap of two acquisitions and
creates a combined data volume.

PXMOD New

 Model for the calculation of MBF maps from dynamic cardiac NH3 PET series. The
model applies a basis function approach and includes right and left ventricular
spillover.

PSAMPLE Improved:

 Calculation of the calibration factor from a single calibration acquisition. Two

areas can be interactively positioned on the calibration curve: one for calculating
the average dark count rate (no activity in catheter), and the other for calculating
the average signal plus dark counts (filled catheter).

Data Formats Improved:

 Interfile: Extension for saving SUV-related information, patient information, and

the image orientation.
 Nifti: Support for multi-layer images added.
 MicroPET: Support for reading pre- and postinjection activities.
 MicroPET: Fixed a problem with reading large Inveon data (>2GB).
 Revision of series date default when the information is not contained in file.
 DICOM Element viewer: supports copy to clipboard.

ATL New:

 Flat view shows seriesDBID and patiendDBID in ATL.

 SOP class of exported data is included in the log.
 ATL ip, version and build date are added to details on application level.
 View of license state extended by the possibility to clean up licenses.

Zürich, Oct. 16, 2012

 PMOD Copyright Notice 35

PMOD Copyright Notice

Copyright © 1996-2014 PMOD Technologies Ltd.
All rights reserved.

The PMOD software contains proprietary information of PMOD Technologies Ltd; it is

provided under a license agreement containing restrictions on use and disclosure and is also
protected by copyright law. Reverse engineering of the software is prohibited.

Due to continued product development the program may change and no longer exactly
correspond to this document. The information and intellectual property contained herein is
confidential between PMOD Technologies Ltd and the client and remains the exclusive
property of PMOD Technologies Ltd. If you find any problems in the document, please
report them to us in writing. PMOD Technologies Ltd does not warrant that this document
is error-free.

No part of this publication may be reproduced, stored in a retrieval system, or transmitted in

any form or by any means, electronic, mechanical, photocopying, recording or otherwise
without the prior written permission of PMOD Technologies Ltd.

PMOD Technologies Ltd

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8006 Zürich
Switzerland
+41 (44) 350 46 00
[email protected]
http://www.pmod.com