Integrated Medical Image Processing Systems, Inc

iMIPS

iMIPS, Inc. announces a system for multi-modality image with 2D and 3D fusion visualization tools for the medical imaging research community.^{*(see note)}  The system complete registration analysis consists of several individual applications that are integrated to aid in the of multi-modal data sets.
 

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Key Features --V1.1

• Buy the whole system or just the application packs you need.
• Introductory Price: $300 - $600/application pack. $3000/complete system.
• No risk: Download the entire system for a free 30 day trial via internet.
• Completely integrated system with point-and-click GUI interface.
• Easy to learn: On-Line Interactive Tutorials, Interactive Step-by-Step Self Running Demos, and Documentation.
• Reads various file formats (MRI, PET, NEMA 2.0, DICOM 3.0, User Defined Templates, ...).
• Automatic segmentation of scalp on structural images. ( about 2 minutes on 256X256X128 data set)
• Various data pre-processing techniques
• Intra- and intermodality multi-volume image registration (fMRI, MRI, CT, PET, SPECT). (from 10 sec to several minutes based on volume size and sampling )
• Interactive 2D and 3D visualization with fusion and excavation.
• Standard Data Output: Compatible with ANALYZE, SPM, etc.
• Create montage of fused/registered images in tiff format.
• Photoshop like public domain image processing program included!!!

Release iMIPS V1.1

This is a maintanance release of the iMIPS system. This release features the following changes:

• Several bugs have been fixed.
• Easier  1-step access to running  the iMIPS demos.
• Manual Registration/Reslicing function added to registration engine
• NEW PLATFORM SUPPORT for LINUX!!!!!

Release iMIPS V1.0

This first release, "V1.0", provides integrated applications designed to speed up and take the frustration out of common tasks in medical imaging research: Quickly convert image data from various scanners (GE, Siemens, etc.) to ANALYZE format. Perform reorientation, resampling and many other standard processes on image volumes. Automatically strip extracranial tissue from structural images with the unique iMIPS "scalper". Perform inter- or intramodality image registration using an intensity-driven, highly accurate algorithm. Visualize your data with flexible 2D and 3D color, monochrome, and fusion techniques. Output presentations as tiff files for slides and photos with iMIPS Montage and MontageFusion applications. A high quality public domain package is bundled to assist in making dazzling layouts in an environment similar to "Photoshop."

See Product Descriptions for in-depth information on each application.

V1.0 was conceived as a set of self-contained application packs. An application pack contains one or more application modules. Each application module addresses a specific need in the image processing chain. Whether you purchase one application pack or the entire system, V1.0 is supplied in its entirety. Any, or all, application packs can be unlocked using the iMIPS license manager. In this way, each application pack may be purchased separately and has the ability to operate as a stand-alone program or together with other iMIPS applications.

Ease of use is achieved by means of carefully designed GUI interfaces that virtually eliminate the need for typed input and provide information about the status of the process, (e.g. what part is executing and/or what the user should do next, etc). Applications may be customized by the use of a PREFERENCES ... feature that, in effect, stores routinely used settings under a mnemonic name. Ease of use is further enhanced by the modularity of the system that allows data to be passed pantyhose index seamlessly from one application to another. Finally, all image volumes and intermediate results are output in the widely used ANALYZE file format, making the iMIPS system compatible with other popular image analysis software.

Documentation and Training

The system is supplied with a complete set of tutorials, demos and documentation that are formatted as "html" documents for use with Netscape 2.0 (or higher) . Demos are interactive self-running applications that give a quick step-by-step overview on how to use each application. Tutorials provide interactive step-by-step instructions on how to use each application but in greater detail than the demos. Sample data is provided for most applications that can be used with the tutorials. The Help system is an on-line reference, organized as frames with indexing to assist in navigating to the desired help topic.

Support

Problems may be reported via email to support@imips.com. Bug fixes will be available for immediate downloading from our web site, www.iMIPS.com. Customers are encouraged to take advantage of the 30 day free trial to assess the suitability of V1.1 for their applications. iMIPS is very interested in your comments on, and nylon stockings experiences with the product, but in order to keep prices low, iMIPS will provide individual support only on a fee for service basis.

Please Note

* iMIPS software is not approved by the USFDA and should not, under any circumstances, be used for patient care applications.

APPLICATION PACK 1

READERS

The iMIPS READER application converts image data written in proprietary image (or other known formats) to a standard format -- ANALYZE. ANALYZE format is the standard for input and output for all iMIPS applications. The READER also provides an easy to use interface to define a template to read other data formats.

 

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KEY FEATURES:

• Direct support for several widely used imaging device formats.
  • SIGNA (General Electric)
  • GENESIS (General Electric)
  • SIEMENS (.ima internal format)
  • ACR/NEMA (2.0, compatible with PHILIPS .ani format)
  • ECAT (6.0 ,7.0)
• Ability to read sequence of images in proprietary formats and combine into volumes and write data as 1 volume/file (e.g. fMRI).
• User-definable formats support many other image file formats, e.g. INTERFILE.
  • Define how data is organized e.g header and data in same file, header and data in separate files etc.)
  • Define how to obtain necessary information from header (x,y,z dimensions etc.) via specifying offsets and/or tags.
  • Define how to obtain and interpret image/volume data.
  • Read and convert and write the data in analyze format.
• Orthogonal viewer system for visual confirmation of successful data conversion.
  • Viewers with ability to pan and zoom and navigate through data with mouse.
• Reads data with nonuniform slice thickness and outputs as extended ANALYZE format (*.hdr, *.img, *.aux).
• Named preferences can be used to customize commonly used settings.

 SCREEN SHOT

APPLICATION PACK 2

DICOM READER

Convert DICOM 3.0 (Part 10) files to ANALYZE format.

 

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KEY FEATURES:

• Reads DICOM 3.0 (Part 10) data files written as one slice per file.
• Reads DICOM 3.0 (Part 10) data files written as one volume per file.
• Lists DICOM header information for confirmation and verification of selected files.
• Ability to read sequence of images and combine into volumes and write data as 1 volume/file (e.g. fMRI).
• Ability to override/add necessary or incomplete values in DICOM files.
• Orthogonal viewer system for visual confirmation of successful data conversion.
  • Viewers with ability to pan and zoom and navigate through data with mouse.
• Reads data with nonuniform slice thickness and outputs as extended ANALYZE format (*.hdr, *.img, *.aux).
• Named preferences can be used to customize commonly used settings.

APPLICATION PACK 3 (ORIENT Any and PROCESS Any)

ORIENT Any

Provides the tools associated with reorienting and reshaping image volumes. Results are shown automatically in the iMIPS ORTHOGONAL VIEWER. Can be used as a pre-processing step to reorient a volume to match the slice orientation of another for the purpose of registration.

 

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KEY FEATURES:

• Orthogonal re-mapping of image volumes.
  • Transpose coordinate axes, e.g. axial to coronal slices.
  • Mirror coordinate axes, e.g. mirror about X axis..
  • Rotation about an axis.
• Crop images.
• Resample to cubic voxels.
• Convert any data type (float, double, short, integer) to byte format.
• Named preferences can be used to customize commonly used settings.

 

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PROCESS Any

Performs image processing/editing operations on an image volume. Results are shown automatically in the iMIPS ORTHOGONAL VIEWER.

 

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KEY FEATURES:

• Input can be any data type (float, double, etc.).
• Input can be non-uniform slice thickness.
• Resampling to any voxel dimensions.
• Data with non-uniform slice thickness can be resampled and output as uniform data (e.g. non-uniform CT scans resampled to uniform slice thickness resampled).
• Thresholding.
• Contrast adjustment.
• Smoothing (2D Gaussian with user defined FWHM in mm).
• Voxel arithmetic (+, -, x, /, sqrt, ^2).
• Data Type Conversion (float, double, short, integer) .
• Manual Slice Editor

APPLICATION PACK 4

SCALPER

SCALPER provides fast automatic tools needed to remove the scalp, skull and meninges from brain images based on mathematical morphology and connected components (about 2 minutes for a 256X256X128 sized volume). It is most often used with structural imaging data, such as MRI or CT, although it may also be used with functional modalities. An automatic scalper is supplemented by a manual editing function. In general, automatic scalping works well with MRI slice thickness <= 3 mm in which there is good contrast between brain and extra-cranial structures.

 

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KEY FEATURES:

• Data conversion to byte format with histogram display for data range selection.
• Optional Pre-Processing include data cropping, reslicing to isotropic, and data re-orientation.
• Automates removal of scalp, skull and meninges from structural brain volume.
• Handles anisotropic data sets with automatic kernel size adjustment based on voxel dimensions.
• Works with 2D and 3D kernels .  
• Evaluate result with two viewers (original data on the right and scalped data on the left) that are synchronized with mouse control which allow the user to view the same slices side by side.
• Manual editor provided for further editing after automatic scalping.
• Fast ray-traced volume rendering with ability to view from any viewpoint .

APPLICATION PACK 5

REGISTER One

Intramodality and intermodality registration, including structural to functional modalities and vice versa. Applications include: MRI, fMRI, PET, CT, SPECT. Intermodality registration performance is improved by segmentation of extracranial tissue from structural image volumes; the use of iMIPS' SCALPER is strongly recommended.

 

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KEY FEATURES:

• Registration is performed with a proprietary extension of the Wood's algorithm, a method that works with voxel intensities rather than brain surface contours.
• Registration is a 3D rigid body transform with X,Y,Z shifts and rotations.
• Fast, fully automatic (10 sec. to several minutes depending on data size and sampling).
• Missing data are well tolerated.
• History of registration parameters is saved as text file.
• Frequently used settings can be stored as a named preference.
• Additional file can be resliced with the same transformation parameters. (Statistical Map)
• A fusion display with controls for contrast, and fusion of registered volumes in orthogonal sections for evaluation of registration accuracy is provided.

APPLICATION PACK 6 (REGISTER Many and PROCESS Many)

REGISTER Many

Inter- and intramodality registration of a series volumes. This application is intended to address the situation in which a series of image volumes must be registered to a reference (standard) volume. Examples include adjustment for subject movement during acquisition of series of fMRI or PET volumes.

 

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KEY FEATURES:

• Multi-file selection browser.
• Registration is performed with a proprietary extension of the Wood's algorithm, a method that works with voxel intensities rather than brain surface contours.
• Registration is a 3D rigid body transform with X,Y,Z shifts and rotations.
• Fast, fully automatic (10 sec. to several minutes depending on data size and sampling).
• Optional data smoothing before registration.
• Missing data are well tolerated.
• History of registration parameters for each is saved as text file.
• Graphs and text file document final registration parameters as a function time (i.e. volume #).
• Frequently used settings can be stored as a named preference.

 

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PROCESS Many

PROCESS Many smooths and averages a series of volumes, features useful as pre- or post-registration operations.

 

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KEY FEATURES:

• Smooth a series of volumes, slice-by-slice, with a two-dimensional Gaussian filter.
• The voxel-by-voxel mean over a series of images.
• A threshold may be set to include only supra-threshold voxels in the mean.
• Frequently used settings can be stored as a named preferences

APPLICATION PACK 7

FUSION VIEWER

Provides interactive tools for visualization and fusion of image volumes in 2D and 3D.

 

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KEY FEATURES:

• A single volume may be loaded as a color or monochrome volume.
• Two volumes that are in register and have exactly the same dimensions may be fused or viewed individually.
• Slice-by-slice display is provided with the iMIPS ORTHOGONAL VIEWER.
• Data may be automatically resampled to cubic (isotropic) voxels to provide appropriate scaling in all projections.
• Independent editable color maps are provided for each volume.
• Ability to adjust contrast for each volume.
• Ability to control contribution of either volume in fusion.
• Ability to switch between color/monochrome and fused images independently in each viewer.
• 3D volume rendering is provided for both single and fused volumes.
  • Pilot view to quickly determine viewpoint.
  • Tools are provided for the excavation of the volume, in order to emphasize important image features.
  • Several types of volume rendering are supported: surface, cutting planes and blended.
  • 3D renderer with automatic adjustment for voxel anisotropy.
  • Rendering with interpolate mode for high-quality output.
  • Axis can be added to 3D rendering to aid visualization.
  • Overall contrast adjustment of output image provided.
  • Ability to set transparency for each volume.
• Any image or rendering can be saved in "tiff" format
• Frequently used settings can be stored as a named preferences

SCREEN SHOT#1           SCREEN SHOT#2

SCREEN SHOT#3          SCREEN SHOT#4

APPLICATION PACK 8 (MONTAGE and MONTAGE Fusion)

MONTAGE

MONTAGE allows the 2D display of slices from an image volume in row /column tiled format. Images can be manipulated and annotations such as labels, titles, orientation etc. can be added.

 

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KEY FEATURES:

• The following controls can be set to generate montages:
  • # rows and columns.
  • slice settings (margins and gaps).
  • slice selection with interactive visualization (start slice, slice skip, direction of skip).
  • slice projection (coronal, sagittal, axial).
  • slice orientation (mirrors, rotations).
  • text annotations with interactive and automatic positioning, font selection, font size.
    • slice positioning labels with automatic increments (mm slice positions etc.)
    • orientation labels . (L-R, A-P, etc.)
    • titles for study, subject, etc. identification
  • image contrast
  • editable lookup table for color mapping
  • image zoom
• Frequently used settings can be stored as a named preferences
• Data output is in tiff format.

MONTAGE Fusion

MONTAGE allows the 2D display of color, monochrome and used slices from two volumes in sequence, row and column layout in any order. Images can be manipulated and annotations such as labels, titles, orientation etc. can be added.

KEY FEATURES:

• The following controls can be set to generate montage of fused data:
  • works with two volumes (color (PET) , gray (MRI) etc.)
  • series, rows or columns layout
  • order of image presentation (color,monochrome,fused,color in grey)
  • independent contrast controls
  • image fusion contribution controls
  • slice settings (margins and gaps).
  • slice selection with interactive visualization (start slice, slice skip, direction of skip).
  • slice projection (coronal, sagittal, axial).
  • slice orientation (mirrors, rotations).
  • text annotations with interactive and automatic positioning, font selection, font size.
    • slice positioning labels with automatic increments (mm slice positions etc.)
    • orientation labels . (L-R, A-P, etc.)
    • titles for study, subject, etc. identification
  • image contrast
  • editable lookup table for colormapping
  • image zoom
• Frequently used settings can be stored as a named preferences
• Data output is in tiff format.

SCREEN SHOT

A "MONSTER" MACHINE :

• Get the full power and speed of UNIX on your PC
  • Scalper processes a 256*256*256 data set faster than HP C-110 system or just as fast as a 195 Mhz R10000 SGI Octane  both with the same memory (256 Meg) and swap configuration (500 Meg).
• Low cost
  • Check Dell/Micron/Gateway for current pricing
  • Single or Dual CPU (Pentium II or Pentium Pro CPU's, you pick speed)
  • Options to use a standard vendor DELL, MICRON etc.
    • We will install LINUX on external disk
    • You pick machine, configuration; ship it to us from your favorite vendor, we add necessary hardware/software and ship it to you ready to go. Fast  1 week turnaround from iMIPS.
• Fully configured and tested with iMIPS software under LINUX
  • You pick machine, configuration; ship it to us from your favorite vendor, we add necessary hardware/software and ship it to you ready to go. Fast  1 week turnaround from iMIPS
• Keep the benefits of Windows
  • Dual Boot configuration
  • Run your favorite Windows applications like Word, Excel, Powerpoint
  • Select Windows NT or Windows 95 or LINUX at boot time
  • Shared disks allow you to share data,images etc. between Windows and LINUX.
    • use iMIPS to make TIFF files and read them into Photoshop or Powerpoint without coping or ftping data.
• Other softwares available for LINUX/WINDOWS:
  • MATLAB, MathCOM, Mathematica, SPM
  • Thousands for GNU/freeware that runs on UNIX system are available
  • Use gcc to compile your existing UNIX apps for LINUX
    • MOTIF, OpenGL, etc. all available on LINUX

Please email us for details.

Supported Platforms

Our system runs on the following operating systems:

Hewlett Packard - HPUX 9.05 and greater

Hewlett Packard - HPUX 10.10 and greater

Silicon Graphics - IRIX 5.3, IRIX 6.2 and greater

SUN Microsystems - Solaris 2.5 and greater .

LINUX -    Kernel 2.0.33  (shipped with Red Hat 5) (other versions  not tested)
                       See below for LINUX specifications.

Recommended System Configuration.

Disk Space:

The iMIPS system requires about 50 Megabytes of disk space for the executables, demos, sample data, and documentation.

RAM :

128 Megabytes. The more the merrier. When working with large data sets the amount on memory available will impact system performance. The iMIPS system will run on systems with less memory, but you must have enough swap space and the performance will be slower. We do not recommend running with less that 64 Megs.

Swap Space :

At least 2.5x the amount of RAM on system.

Shared Memory :

Shared Memory usage by iMIPS is on by default and is highly recommended. This is the default with most unix systems. The iMIPS system can be configured to run without shared memory very easily but will require a lot of system resources (memory and swap space).

Color Graphics Adapter :

The iMIPS system can run on most 8,12,16, 24 and higher bit color graphics adaptors. We strongly recommend a 24 bit adaptor for high quality visualization.

LINUX:

We have tested Linux under the following configurations:
 

 Dual Pentium Pro 200 MHZ SMP system with 256 Meg Ram, 500 Meg swapspace, with  3Com 10/100 BaseT network card, Matrox  Millenium 4Meg Graphics card running MetroX  24-bit X-Window server,  Adaptec 2940 UW scsi card, Sound Blaster Awe 32 Sound Card. The system is configured to boot Linux 2.0.33 , Windows NT 4.0 and Windows 95 (user selects when system is booted -- only one operating system at a time though!!) .

Packard Bell Platinum with Pentuim 200 MMX, 64 Megs RAM, 4 Gig ide disk, 128 Meg swap, ccom 3C509 Combo network card, Matrox Millinium II Graphics card running Accelerated X 4.1 (CDE 1.1) 1152x864x24bit  X-Server (24/8 bit) .The system is running Red Hat 5 LINUX.

Mesa OpenGL libraries are needed for iMIPS to run. These are available from your LINUX vendor  or from the MESA website or we can provide these libraries on request.

MOTIF libraries are need to run iMIPS. We can provide a statically linked version on request.
 

System configuration changes:
 

The standard kernel has a very small shared memory segment size. This needs to changed to 64 Meg or greater. The change requires manual editing (very simple) of kernel source and recompliing and reinstalling the kernel. A local LINUX users group is the best place for assistance on this. We can provide instructions but your configuration will differ from ours.

If you have more than 64 Megs of RAM, the boot loader (lilo) needs to be configured to see more than 64 Megs. This again is very simple and we can provide detailed instructions.

 

Installation Instructions :

 

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1. Confirm that you have enough disk space.
   • Applications: ~50 Megs.
2. Select a installation directory on your system under which the system will be installed
   • Create this directory
   • The system will be installed in a subdirectory called "imips" under this selected directory.
   • The IMIPS_PATH environment variable that will be used by the system will be set to selected directory/imips
3. We assume you have downloaded the iMIPS system. If not, please do so by following this link.
4. Move the downloaded file to the installation directory
5. Uncompress the downloaded file using gunzip
   • gunzip imips_xx.tar.gz (xx is the platform)
6. switch user to root (necessary to preserve permissions on various internal files)
7. Untar the imips_xx.tar file
   • tar -xvpf imips_xx.tar
8. This will create an imips subdirectory with the iMIPS system installed.
9. You can remove the imips_xx.tar file when the system have been run

INSTALLATION COMPLETE

At this stage the IMIPS system will not run without valid license file.

Example on installation procedure:

To install imips in /usr/local/imips:

• mv imips_xx.tar.gz to /usr/local
• cd to /usr/local
• su root
• gunzip imips_xx.tar.gz
• tar -xvf imips_xx.tar

iMIPS is now installed in /usr/local/imips.

IMIPS_PATH now refers to /usr/local/imips.To set the IMIPS_PATH environment variable to point to the location where the system was installed

C-Shell: setenv IMIPS_PATH <installation_path>/imips (/usr/local/imips)

Bourne shell: export IMIPS_PATH=<installation_path>/imips (/usr/local/imips)

type $IMIPS_PATH/bin/imips to run the imips system or cd to $IMIPS_PATH/bin and then type imips.

 

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Obtaining 30 Day demo license file:

• cd to the iMIPS installation subdirectory. cd to bin subdirectory and run imips_hostid.
• This will provide the necessary output that you need to email us (hostid) .
• Please email this information to support@imips.com and we will email you back the license file.
• Read the README.txt file in the iMIPS subdirectory for instruction on license installation and iMIPS usage.

 

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Obtaining Permanent license file:

If you decide to purchase the system, please fill out the Order Form on the iMIPS web site.

• cd to the iMIPS installation subdirectory. cd to bin subdirectory and run imips_hostid.
• This will provide the necessary output that you need to fill hostid on the order form.
• Fill out the order form on the iMIPS web site.
• We will reply with confirmation for your order.
• We will email you the license file when we recieve payment.

  Read the README.txt file in the iMIPS subdirectory for instruction on license installation and iMIPS usage.

 

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Installing iMIPS License File:

Once you recieve email from support@imips.com. Please cut out the license information from the email and save it to a file named imips_license.

Copy this file to the $IMIPS_PATH/env directory. You must be root to do this.

Start iMIPS :

$IMIPS_PATH/bin/imips

Add $IMIPS_PATH /bin (the actual path) to your PATH variable to allow you to run iMIPS by just typing imips.

 

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iMIPS Help:

The iMIPS, Inc. help system uses Netscape as its basic engine.

Please install Netscape 2.x or 3.x on your system to use help facility. iMIPS help will NOT work with the newly released Netscape 4.x.

Please note that the path to netscape needs to be in your PATH variable. To verify, type "netscape" at the unix path. If netscape starts, you can use the help system without any further modifications, if not you need to modify your shell's resource file to add netscape to your PATH variable.

 

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Adjusting System Parameters:

The iMIPS system can have several user defined parameters that can be set to modify the system to fully utilize the hardware it is running on.

You can ONLY modify following parameters in the file: $IMIPS_PATH/avs_stuff/runtime/avsrc

#Colors r g b gray

This option controls how many cells of a system colormap iMIPS willattempt to allocate to itself when it starts. r g b gray represent numbers for red, green, blue and gray. This is primarily intended for people who are using AVS from X terminal, or Pseudocolor workstation that object to the number of colormap cells that iMIPS tries to allocate for itself.

Colors can be used to increase the number of colormap cells iMIPS allocates.

#Gamma 1.0

Controls the brightness of the display for all windows. The default varies from platform to platform and monitor to monitor. Values between 0.5 and 2.2 are good starting points for experimentation. Higher real values produce a lighter display. We encourage to use this to control overall contrast of the iMIPS system.
 

VisualType TrueColor

This command may be necessary when you are seeing less color rendition than you know your display is capable of. iMIPS will present a warning if the visual that is being used is insufficient. iMIPS nomally ships with a TrueColor visual. This we find works best on most systems. If you comment this line, iMIPS will use the X server's default visual. The standard S windows command to list which X visuals are available is xdpyinfo.

Visual Type lets you specify a visualtype, either PseudoColor, TrueColor, or DirectColor.

#VisualType VisualID 0xnnnn

We recomment that you use this version of the resource to set the visual that is used by iMIPS. This version give you the most control in setting the visual that is used. Use the xdpyinfo command to list all the possible visuals on your X server. The last several visuals are usually the best visuals that are available on your X server. The output of xdpyinfo will list the VisualID of each visual. To set a specific visual to use, substitute this ID value for the 0xnnnn on the resource line and uncomment (remove the #) on this line. You might need to comment (add #) to the beginning of the other VisualType resource line.

ScreenSize 1280x1024

Specifies the size of the iMIPS virtual display in pixels, confining iMIPS to run within this area. iMIPS scales its interface to fit the virtual screen. This is useful if you have a smaller or bigger screen.
 

 

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