Activate Dicom Editing Osirix Free

Osirix Mac
Osirix For Windows

Configuration of Osirix¶ In Preferences-Listener, activate and configure AETitle and Port (e.g. In Preferences-Locations, add a DICOM Node: with the AET of your Orthanc instance (default is ORTHANC) with a name (eg MYORTHANC) with Retrieve method C-GET; with Send Transfers syntax: Explicit Little Endian. OsiriX permits one to edit any particular field in the DICOM header. This is a three-step process as indicated below: Activate the editing function by clicking on edit. Double-click on an entry to edit it and hit return. Edit other items as necessary. Click Apply specifying the Study level so that all the Series of the Case are changed.

[ChimeraX DICOM index]

DICOM Viewers

Viewers

← Viewers

See also: I Do Imaginglist of free medical imaging software, especiallyMac DICOM display

Medical Holodeck
- DICOM viewer for VR (Vive, Oculus Rift, Windows mixed reality HMDs:Samsung Odyssey, Dell Visor, Lenovo Explorer, Asus Windows, Acer Windows)
- versions: free, basic ($75/mo), pro ($250/mo), cloud ($290/mo);paid versions have 30-day free trial
Horos
- free and open source (LGPL-3.0) but no free documentation; Google group forum not that extensive
- macOS 10.11+ only, not Windows or Linux
- more...
  - for some reason, I cannot download from Firefox (dmg stays at size 0 forever), but download from Safari is fine
  - at least to novice, Horos and Osirix Lite interfaces seem very similar(organization, layout, options and corresponding icons)
  - File... Import allows selecting a stack of DICOM files or a folder from which multiple stacks found in subdirectories can be opened
  - datsets are saved in a Horos database as either file copies or links, then automatically reopened upon next use unless explicitly deleted from that database
  - to get to volume visualization from the initial database window:
    - click 2D Viewer icon top middle of database window
    - from the resulting 2D viewer, choose menu item 3D Viewer... 3D Volume Rendering (other choices include MPR options, 3D MIP, 3D Surface Rendering)
    - top bar now allows choosing CLUT or 3D Preset, level of detail, shading, parallel (orthographic) vs. perspective, filtering, etc.:
    - a 3D preset (seeplist files in repository)includes not just a CLUT but other settings likeprojection mode, background color, shading, and filtering... perhaps moreeasily understood by clicking Info on the 3D preset browser in Horos
    - show histogram w/ thresholds by double-clicking certain entries in the 3D preset browser (I guess the ones with xy pairs in the plist file, e.g. Airways II, Gold Bone, Soft + Skin, rather than just a reference to a separately defined CLUT, e.g. Glossy, Mid Contrast, Red on White)
    - CLUT plist files also in repository
    - current state can be saved as a 3D preset
  - mouse modes:
    - defaults: middle mouse translates, right mouse zooms, (left) click-drag adjusts windowing (vertical WL, horizontal WW, diagonal both) in 2D viewer, XY-rotates in 3D viewer; scrolling goes through planes in 2D viewer (Mac trackpad click-drag +cmd does translation, +alt windowing, +shift zoom, +ctrl windowing in 2D, Z-rotation in 3D)
    - * values for WL, WW, zoom, etc. reported continuously in text (and color key labels, if color key shown) on window
    - in 2D viewer, cursor position is also reported continuously
    - 3D volume-viewer icons for changing left-mouse function:
      ...from left to right, based on experimentation: windowing (WW/WL), XY-translation, zoom, Z-rotation, XY-rotation, rotate around cursor position (? not good because I haven't figured out howto translate in Z), measure distance, add marker, draw circle (maybe it selects contents for later actions but haven't figured out what), hand-draw arbitrary closed shape (again presumably to do something else later), bone removal based on values specified in secondary dialog
    - 3D surface-viewer mouse modes are only zoom, translate, rotate, center of rotation, and mark; threshold level, resolution (step), and smoothing are set in a secondary dialog, and with smoothing it may not be fast enough for a thresholding mouse mode
  - * orientation cube labeled A(nterior), P(osterior), L(eft), R(ight), S(uperior), I(nferior)
  - * the cropping box has a little ball in the center of each side for grabbing/dragging
  - show color key in 2D viewer with 2D Viewer... Color Look Up Table Bar
  - Horos plugins include fairly simple map operations, calculations, and converting other image formats to DICOM
  - single-DICOM-file segmentations seem to be ignored (subset of RIDER Lung data from TCIA [zip file]), if I import a directory with both segmentation(s) and a corresponding image stack, I only see the image stack in the database, and even if I explicitly import a single segmentation file, nothing seems to happen.
    1/22/2019 I can create a segmentation using the 2D viewer menu ROI... Grow Region (2D/3D Segmentation) and save it as a .roi (2D) or .rois_series (3D) file (poorly made example that goes with the lung dataset) that can be read back into Horos. If it's a 3D segmentation, then ROI... Compute Volume can be used. It thinks a while and then shows a results panel with options including opacity and “Save as DICOM” but unfortunately that only refers to a single 2D image. Saving lists the image in the database window from where it can be exported to a DICOM file, but again, it's just one 2D image. Can mask data with the 3D segmentation (ROI... Set Pixel Values to). Youtube video not in English but shows some of this stuff.
  - my example time series (subset of mouse brain astrocytoma MRI from TCIA [zip file]) is just intepreted as a really big stack, but maybe some other steps are needed to treat/mark as 4D. Clicking the “4D Viewer” icon says that multiple series taken at different times are needed as input (whereas my example series that is 600 .dcm image files all in one directory seems to be misinterpreted as one big series with multiple mouse heads stacked together). (In Horos, had the same problem with the time series example linked to the Slicer MultiVolume Explorer documentation, see below)
  - 1/29/2019 Horos displays RTDOSE, RTPLAN (as in the Head-Neck-Cetuximab study from TCIA) as black-and-white stripes in preview/thumbnail, and trying show them in the 2D viewer gives “no files available (readable) in this series”... although thumbnail images are shown for the CT and RTSTRUCT “from rtog conversion,” trying to show them in the 2D viewer gives the same complaint
OsiriX
- OsiriX MD commercial, OsiriX HD for iOS, OsiriX Lite free version
- recent macOS, supports 64-bit computing and multithreading
- basic tutorials available for free, advanced for $$
3D Slicer (see alsothe wikiand forum)
- open source “BSD-style” license, NIH-funded
- 3D Slicer as an image computing platform for the Quantitative Imaging Network.Fedorov A, Beichel R, Kalpathy-Cramer J, Finet J, Fillion-Robin JC, Pujol S, Bauer C, Jennings D, Fennessy F, Sonka M, Buatti J, Aylward S, Miller JV, Pieper S, Kikinis R.Magn Reson Imaging. 2012 Nov;30(9):1323-41.
- more...
  - various filtering options
  - interactive and automated segmentation tools
  - rigid and non-rigid registration (superposition)
  - surface-model creation and manipulation
  - users can save scenes (something like sessions?), each potentially containing multiple scene views
  - native formats: Slicer scene file is MRML (medical reality modeling language), saved with data as a MRB (medical reality bundle) file. From using the program, looks like the primary option for saving individual image series and segmentations is NRRD (nearly raw raster data). Several other formats also read, tiff, jpeg, vtk, ...
  - I tried Slicer 4.10.0 on Mac (desktop and laptop)
  - startup quite slow, on desktop always asks if I want to install Xcode
  - many tutorials (the PDF slideshows seem nice, the videos vary), including:
    - 3D Visualization of DICOM Data
      to display DICOM there are two steps: import the data, then load it from the Slicer DICOM database
      Volume Rendering module has several presets
      the volume rendering becomes low-resolution during manipulation
      in this interface, ROI means a cropping box; the little squares are “handles” to drag the box faces or translate the box in any 2D view or the 3D view
      if you miss the little square in the 2D view, dragging will instead change windowing: WL (vertical) and/or WW (horizontal)
      then turning volume rendering on by clicking the eye icon only does it within the smaller ROI
    - also viewed Quick Start Guide (mainly justhow to install), Welcome, 4-Minute Tutorial for first-time users(looks like more than 4 minutes and mostly showing pre-made VTK surface models,but interesting)
  - module documentation includes:
    - Segmentations“It is important to remember that segmentations are not labelmaps”
    - Segment Editor – apparently meant to replace Editor(opening Editor shows message to use Segment Editor for more advanced editing)
    - Editor – manual segmentation; labelmaps are related to,but not (as mentioned above) the same thing as segmentations
  - single-file segmentation DICOM (examples in the RIDER Lung data from TCIA [zip file]) is recognized on import, Modality: SEG in the Slicer DICOM browser; a dialog appeared to suggest I get the Quantitative Reporting module...
    - Extension Manager can be opened by clicking the “E” icon on Slicer window top right.
    - QuantitativeReporting depends on other extensions: PETDICOMExtension, DCMQI, SlicerDevelopmentToolbox, so I clicked to install them all.
    Upon Slicer quit/restart, the segmentations were loaded successfully into the viewer. The example data folder included 2 scans '4' and '8' and a bunch of segmentations, which were aligned to '4' ('8' was offset). In the Volumes module I could delete '8', leaving just the one aligned with the segmentations.
    I tried making my own segmentation in Slicer, as in this video tutorial. There are lots of options, including those analogous to Volume Eraser and Hide Dust. Segmentation save format is only NRRD, and export format choices are only STL and OBJ. Saved NRRD file could be read back in, and was automatically listed as a segmentation. Exported STL file (coordinate system choices LPS or RAS, I chose the default LPS) could be read back in, but was listed as a separate model, not a segmentation, and was not aligned.
    1/19/2019 In the RIDER Lung segmentation DICOM file metadata, manufacturer and software version refer only to Slicer, but the manufacturer model field gives the URL for the Quantitative Reporting module, which sounds like it can save DICOM segmentations. I couldn't use it to save the segmentation opened from previously saved NRRD (error: empty segmentation), but I could save one made in the current session or one previously read from DICOM (RIDER Lung). However, “saving” in this context only means adding it to the internal Slicer DICOM database (SQL), where the RIDER lung segmentation was already. Since the database contents persist through quitting/restarting Slicer, this process at least allows saving my segmentation for later use in Slicer, but doesn't produce a file that can be used in some other program. The Slicer database dialog has an Export button for writing DICOM, but its balloon help says “not yet available” (even in daily build 1/18/2019) and trying to use it anyway gives “Error occurred in exporter” message.
    I see another video tutorial showing a different set of steps for saving segmentations + volume to DICOM. I followed that entire workflow which worked up to clicking the Export button, which did absolutely nothing, as far as I could tell. However, in the video looks like I need a DicomRtImportExport plugin or something like that. I didn't find exactly that plugin name, but I installed one named SlicerRT (and TCIABrowser too since it interested me). Restarted, repeated the entire process, still got error or nothing exported.
    1/20/2019 Got a little farther: if I choose export format RT, I can export a study “to DICOM” using the workflow shown in that video, but only to the Slicer DICOM database and only as modality RTSTRUCT, not SEG. Export type DICOMSegmentation seems to either cause error or do nothing, export type Scalar Volume only exports the images, not the segmentation. Again, no actual DICOM output files, only export to the Slicer DICOM database. The only way I found to get SEG into the database is with the Quantitative Reporting module, as reported above.
  - time series (subset of mouse brain astrocytoma MRI from TCIA [zip file]) was read without error messages; need to investigate further.
    1/22/2019 Now I see it is loaded as a 50-frame “multivolume,” apparently their term for a time series, in agreement with the 50-frame time slider in ChimeraX, and can be played using the MultiVolume Explorer module. Another example time series (prostate) is provided in that module's documentation.
  - 1/29/2019 Slicer displays RTDOSE as colored blobs if associated RTPLAN is also opened, RTSTRUCT as colored overlay if associated CT is also opened
    2/12/2019 Slicer can render RTSTRUCT in 3D as lines or multiple transparent surfaces, in addition to the overlays on the 2D slice views. Settings/options for creating surfaces from contours are described in the Segment Editor documentation.
MRIcro family of programs
- open source BSD license, NIH-funded
- MRIcroGL real-time interactive volume rendering, requires modern graphics card (Windows, Mac, Linux)
  - these Mac downloads each include two versions:
    - [Nov 2018 github] ...includes MRIcroGL and MRIcroMTL (uses Apple's Metal instead of OpenGL)
    - [Jun 2018 NITRC] ...includes MRIcroGL and MRIcro for OSX which I guess has lower graphics demands (for macOS 10.7+ 64-bit Intel), manual for MRIcroGL (PDF, Jun 2017), and several sample datasets and templates for overlays
    - MRIcroGL is different in those two downloads: color-scheme menu in a different place, the github one has fewer import options and shader options, etc.
  - GLSL volume ray casting rendering
  - ...* surface renderings do look really nice
  - formats: primarilyNIfTI (Neuroimaging Informatics Technology Initiative: .nii, .nii.gz, .hdr/.img).Release notes also mention importing other formats:Freesurfer images (MGH/MGZ format), NRRD images (NRRD/NHDR format), AFNI (HEAD format), VTK/ITK MetaIO format (MHA/MHD), TIFF/LSM/OME.
  - does not read DICOM directly, comes with slightly unfriendly (command-line) DICOM → NIfTI converter ...apparently this conversion is quite complex, the author even wrote a paper about it in 2016
  - video tutorials page links broken but a few are available at Chris Rorden's YouTube channel
  - full colormap control for rendering different tissues differently
  - shaders are text files, users can create their own custom combinations
  - Pascal scripting
  - I tried MRIcroGL on 2015 MacBook Pro and 2012 iMac running High Sierra (10.13): nice graphics, smooth response to manipulation, LOTS of rendering options, sliders for individual parameters, many built-in color schemes (some with intensity values for specific tissues in CT), clipping, cutouts (box-shaped), slice views, overlays ...
  - with both program versions, trying to change color scheme for the “visible human” dataset didn't change its appearance, but other example datasets didn't have this issue... maybe because that dataset consists of thin-section (color?) photographs rather than monochrome imaging
  - automatically remembers/opens last data, opening something else replaces it
  - as far as I can tell, one program instance shows one dataset (potentially with overlay(s)), but multiple instances can be run simultaneously and “yoked” to synchronize slice display
  - click-drag rotates, orientation cube shown, scrolling zooms (up to a limit); no panning?
  - use keys a(nterior), p(osterior), l(eft), r(ight), s(uperior), i(nferior) to move slice plane
  - prefer Chimera(X) interactive clip translation/rotation over the 3 sliders
  - * useful predefined color scheme values for specific tissues (see below)
  - * nice color key automatically shown/updated (yet optional)
  - used the DICOM → NIfTI converter on one of the Belarus chest datasets; got some errors/warnings, some .nii output didn't look right, but the last/largest one appears to have all the data: bones, lungs and other tissues shown nicely with the appropriate color schemes
  - tried to import Allen Inst. OME TIFF but got error about incompatible compression type
  - update 2 September 2019: latest release supports drag-and-drop to open DICOM folders! Also has expanded TIFF support (now can open my Allen Inst. OME TIFF example) and Python scripting.
Web-based viewers:
- OHIF (Open Health Imaging Forum)
many basic Windows-only DICOM viewers that I won't bother to list here

← Acronyms & Terminology

← Feature Lists

Potential tasks for medical image analysis:

view header information
anonymize
zoom, rotate, flip
invert dark/light
adjust contrast and brightness
color processing, color mask
adjust windowing/thresholding #1613
12/17/18 Darrell mentions 'color lookup table (CLUT) editor,' HOROS has mouse modes to adjust:
- leveling - moving thresholds in parallel along histogram
- windowing - narrowing/broadening visible range of data values (moving bounding thresholds in opposite directions)
12/17/18 text in VR to report the threshold levels#1614
(Elaine: maybe labeled color key as inMRIcroGL or Horos,WW/WL values as in Horos)
(related: Phil mentions popup reporting data value at voxel like HOROS)
built-in color schemes:
- HOROS 3D presets (he often uses Airways II)
convert data types, formats
filter (smooth, sharpen, etc.)
other data editing (copy, paste, erase?), Chimera Volume Eraser
clipping
mark points and regions
select regions, potentially of irregular shape
detect/mark edges, boundary surfaces; mask and segment
12/17/18 Beth and Darrell mention segmentation, particularly by hand marking
annotate (text or geometric objects in image, metadata outside of image)
geometric measurements (distance, angle, area, volume, etc.)
data measurements (mean, SD, min, max, plot values along an axis, etc.)
texture analysis (not sure what this means)
play time series, save movie files
compare datasets (with and without contrast agent enhancement;before, during, and after therapy; normal vs. abnormal brain; etc.)
overlays (annotations, localized brain activity, etc.)
registration with atlases/templates (anatomical landmarks, referenceorgans) or between multiple datasets, rigid or non-rigid (with scaling/warping)
along those lines, medical image fusion...essentially 3D superposition of multiple datasets or maps
fetch data from public sources

Other desirables from discussion:

Activate dicom editing osirix free download

Osirix Mac

large data performance, especially in VR
multi-user VR meeting
working with multichannel data, e.g. annotations from AI/deeplearning may be saved as color channels to be overlaid on the exptl. dataset

← Public Sources of Files and Info

The Cancer Imaging Archive (TCIA) has many collections ofdatasets (public collections also listed onthe wiki)
- formerly the National Biomedical Imaging Archive (NBIA)
- downloading requires NBIA Data Retriever app
- however, there's also aREST APIfor programmatic access
Patient Contributed Image Repository(only 10 downloads)
MedicalImage Samples (only 5 multiframe sets)
open-access medical image repositories – a big list,but images are not necessarily in DICOM format
NIH DeepLesion dataset – over 32,000 annotated lesionsin CT images available via Box, but currently only PNG format

Mostly info:

Osirix For Windows

David Clunie's Medical Image Format Site(some files in Images section near bottom)