I'm working on a project where I need to generate an IFC file, and am given not much more information than geometry (I have access to the density and heat-conductivity of materials, and basic labeling for Objects).
So far I could only find what IFC can store, never what IFC needs to store.
What do I need to include in an IFC file so it is properly functional?
What does an IFC file need besides basic geometry?
Disclaimer: I have not read (or bought) the standard. My knowledge primarily stems from working with IFC files and trying different things. And reading the buildingSMART documentation. So I can't give you a hard guarantee, but I am rather confident my information is correct/usable.
As an alternative to buying the official standards file, you could look into the official documentation by buildingsmart. (Also have a look here for more general information and availability of other/more modern releases).
Now assuming you are familiar with the basic STEP file layout (header and data segment), let's jump to what an IFC file absolutely has to include to be considered correct (as far as I understand the documentation; there might be parsers/loaders which can load incorrect/incomplete files, but we aren't aiming for them). Also note I am building this example for IFC 4.0. This should be correct for the current IFC 4.1 standard, but probably not for the older IFC2X3 standard (there have been some relaxations in IFC4 from IFC2X3). Also I am skipping on names and descriptions - you can set those fields for testing to recognize your structures in a viewer (it's easier than comparing GUIDs).
IfcProject
The root of all elements is the IfcProject. It also contains most basic properties and definitions for all other elements. The attributes required per documentation on this entity are only the unique id. But for a working example you usually also need a minimal unit assignment and representation context.
#20= IFCPROJECT('344O7vICcwH8qAEnwJDjSU',$,$,$,$,$,$,(#19),#13);
In the unit assignment you define required units, starting from geometric units to monetary, thermal, etc. The minimum is length, area and angle to meaningfully define geometric items. So for our example we include only those: metre as length, square meter as area and radians as angle. If you need foot or inch or degree you can define those as derived units.
#10= IFCSIUNIT(*,.LENGTHUNIT.,$,.METRE.);
#11= IFCSIUNIT(*,.AREAUNIT.,$,.SQUARE_METRE.);
#12= IFCSIUNIT(*,.PLANEANGLEUNIT.,$,.RADIAN.);
#13= IFCUNITASSIGNMENT((#10,#11,#12));
The representation context defines for a given class of representations (=geometric/parametric descriptions) the basic coordinate system. So the simple case would be a 3-dimensional right handed system at point zero. IFC is working with the z-axis pointing up - this might be important if your are working with models/files originating from 3D/OpenGl applications which usually assume the y-axis pointing upwards. You also need a precision value - I am using 1.0e-5 here, but you might want to test out if you can go with less or need more. The precision is usually applied when comparing points/edges when combining geometry (during constructive solid geometry steps). If you have errors, try a different precision value.
The second attribute of the representation context is the context type. This is a string identifying on which representations this context should be applied. The documentation states that values are based on "implementers agreement" - which means AFAIK "look what the others are using". From my experience using "Model" works for 3D geometry. Using "Plan" for 2D plans and sketches should work, too.
#14= IFCDIRECTION((1.,0.,0.));
#15= IFCDIRECTION((0.,0.,1.));
#16= IFCCARTESIANPOINT((0.,0.,0.));
#17= IFCAXIS2PLACEMENT3D(#16,#15,#14);
#18= IFCDIRECTION((0.,1.));
#19= IFCGEOMETRICREPRESENTATIONCONTEXT($,'Model',3,1.0E-5,#17,#18);
Spatial container for elements
Elements can't be added to the IfcProject directly - they need to be placed into a spatial element which is contained in the project. There are three possible choices: IfcSite, IfcBuilding and IfcSpatialZone (see section Spatial Decomposition on the IfcProject page). The IfcSpatialZone is defined as non-hierarchical spatial element - its usage is slightly different from the other two (elements are added using a different relation).
A single site is sufficient as spatial container. Adding all elements to it might be sematically vague (mostly fences are directly added to it, other elements are usually inside a building) but not incorrect. (IFC does not care if you have electrical appliances in your garden). As nearly all attributes of IfcSite are optional we can skip on those. But beware: if you give your site a representation (=some geometric shape) you will need to include a placement for it. The site will be aggregated into the project to be related to it.
#30= IFCSITE('20FpTZCqJy2vhVJYtjuIce',$,$,$,$,$,$,$,.ELEMENT.,$,$,$,$,$);
#31= IFCRELAGGREGATES('0Du7$nzQXCktKlPUTLFSAT',$,$,$,#20,(#30));
Elements
Actually that is all that is needed as absolute minimum structure. Now you can add your elements - entities of some type derived from IfcProduct. As all those elements have some sort of meaning attached to it you either need to select those closely matching the objects you have, or you might want to use IfcBuildingElementProxy which is the most "meaningless" (or better: no specialized semantic meaning) object type. The following code places one proxy without geometry. The placement references the same coordinate system definition that is used to create the coordinate system out of convenience as it doesn't transform or move anything. Your geometry would be added through a product definition shape which has shape aspects and finally some geometry items. The building smart documentation has a few examples with assigned geometry.
#40= IFCLOCALPLACEMENT($,#17);
#41= IFCBUILDINGELEMENTPROXY('3W29Drc$H6CxK3FGIxjJNl',$,$,$,$,#40,$,$,.NOTDEFINED.);
#42= IFCRELCONTAINEDINSPATIALSTRUCTURE('04ldtj6cp2dME6CiP80Bzh',#12,$,$,(#41),#30);
Conclusion
So there isn't much needed as bare minimum to add elements:
a project
basic unit definitions
one spatial container
The complete example file would be:
ISO-10303-21;
HEADER;FILE_DESCRIPTION(('IFC4'),'2;1');
FILE_NAME('example.ifc','2018-08-8',(''),(''),'','','');
FILE_SCHEMA(('IFC4'));
ENDSEC;
DATA;
#10= IFCSIUNIT(*,.LENGTHUNIT.,$,.METRE.);
#11= IFCSIUNIT(*,.AREAUNIT.,$,.SQUARE_METRE.);
#12= IFCSIUNIT(*,.PLANEANGLEUNIT.,$,.RADIAN.);
#13= IFCUNITASSIGNMENT((#10,#11,#12));
#14= IFCDIRECTION((1.,0.,0.));
#15= IFCDIRECTION((0.,0.,1.));
#16= IFCCARTESIANPOINT((0.,0.,0.));
#17= IFCAXIS2PLACEMENT3D(#16,#15,#14);
#18= IFCDIRECTION((0.,1.));
#19= IFCGEOMETRICREPRESENTATIONCONTEXT($,'Model',3,1.0E-5,#17,#18);
#20= IFCPROJECT('344O7vICcwH8qAEnwJDjSU',$,$,$,$,$,$,(#19),#13);
#30= IFCSITE('20FpTZCqJy2vhVJYtjuIce',$,$,$,$,$,$,$,.ELEMENT.,$,$,$,$,$);
#31= IFCRELAGGREGATES('0Du7$nzQXCktKlPUTLFSAT',$,$,$,#20,(#30));
#40= IFCLOCALPLACEMENT($,#17);
#41= IFCBUILDINGELEMENTPROXY('3W29Drc$H6CxK3FGIxjJNl',$,$,$,$,#40,$,$,.NOTDEFINED.);
#42= IFCRELCONTAINEDINSPATIALSTRUCTURE('04ldtj6cp2dME6CiP80Bzh',$,$,$,(#41),#30);
ENDSEC;
END-ISO-10303-21;
Note that loading this one up doesn't show anything, because it doesn't contain any geometry. Also please note that I have not yet verified if it is error free - I currently don't have my IFC tools at hand (if you would like to verify your files have a look at stepcode which can check if your files are syntactically correct - it won't check semantic meaning or enforcement of the mentioned concepts in the building smart documentation.)
Also good to know is that the order of references/ids (like #20) can be freely arranged - you can reference elements that you add later in the file and the references only need to be unique to this one file. This means the lines of the example file can be shuffled and it is still a valid file - parsers usually use a two-step apporach to create an in-memory representation (1. parse into IFC classes, 2. resolve references).
I'm using ITK-SNAP to compare the intensities of several Regions of Interest between several conditions.
For some subjects, I need to realign one image to another by using the Registration tool.
However, I noticed that the intensity values of a specific segmentation that I drew on the reference image doesn't change no matter how I register.
The value will be different between the two images, but even if I manually register the second image to something completely off, it will stay the same.
Is it possible to get the actual mean intensity of my segmentation depending on where it is on the registered image ?
Segmentation menu, option "Volumes and Statistics..." should show you what you are looking for.
Registration does not impact the intensity. Depending on how you transform your image, it affects the location and coordination of your voxels! It does not play with the intensities! It may reform, or reshape, rotate, or translate the image. If you expect different intensities after registration, you need to apply some other techniques rather than registration! because all the transformation matrix are applied on the coordination and location. You should play with the other features of your data!
There are some registration methods which influence the intensities but they are not used in ITKSNAP for example. You should look for its special package.
For example this paper is on:
Intensity based image registration by minimizing the complexity of weighted subtraction under illumination changes
Which is specifically playing with the intensities for fusion.
https://www.sciencedirect.com/science/article/abs/pii/S1746809415001755
Other example is this matlab script for Intensity based automatic registration, The process begins with the transform type you specify and an internally determined transformation matrix. Together, they determine the specific image transformation that is applied to the moving image with bilinear interpolation.
https://www.sciencedirect.com/science/article/abs/pii/S1746809415001755
If a patient is scanned in the axial plane and the Patient Position attribute reads 'HFS' or head first supine, then shouldn't the Image Orientation (Patient)(0020,0037) attribute be [-1,0,0,0,1,0]? It seems it should be [1,0,0,0,1,0]. My confusion might lie with an incorrect understanding of what the 'scanning viewpoint' (technical name for this?). Hopefully this image clarifies what I mean:
If the 'scanning viewpoint' is the 'Neuro-Surgeon's' view then the attribute should read [-1,0,0,0,1,0]? I thought that this should be the case if the Patient Position attribute reads 'HFS'. If somebody can clarify I would be very gateful!
Sorry. I had to update my answer as I overssimplified and made a relation between the two attributes while there really is none. The answer was accepted in the meantime but I decided to update the answer anyway for future reference.
#OP sorry the answer is a bit more complex.
In case of HFS the patient is positioned exactly as in your image. Patient Position (0018,5100) specifies the position of the patient relative to the imaging equipment space when facing the front of the imaging equipment.
The different view points mentioned in the OP are the two main viewing conventions. Viewing convention is not part of the DICOM standard. DICOM-compliant scanning devices transmit pixels for radiological viewing convention. The scanning device orders the pixels depending on the patient orientation during the scan. Hence, the image technologist must indicate the patient orientation before scanning starts.
//edit
More correct but technically more complex answer. The two dicom attributes are not related. The Image Orientation Patient is related to the patient body, regardless how she's placed in the machine, while Patient Position specifies the position of the patient relative to the imaging equipment. The machine manufacturer has to know the Patient Position to be able to calculate the Image Orientation (Patient) from the image orientation cosines in the frame of reference of the machine.
Knowing this we can now determine what image orientation patient means. The vectors first component specifies the direction of the first row of the image with respect to the patient coordinate system. Similarly, the second component of the vector specifies the direction of the first column of the image. We now define the image orientation patient as the rotation matrix P used to describe patient orientation in the DICOM coordinate system. **now, in the default CT case you typically have the scenario as shown in the image above. Where HFS is [1 0 0; 0 1 0]. However, MR almost never has identity for the Image Orientation patient but typically has a slightly angularjs set of axes. Note that both cases would still have HFS as their default.
When I receive scout images, where I can find the x-tube angle information from the DICOM header? Basically I need to know the scout was taken when x-tube is at the top or it is at the 90 degree or any other degree.
The precise answer to your question depends on the type (SOP Class UID) of DICOM object that your question refers to. AFAIK, the tube position is never encoded in DICOM headers, however, what you probably want to know is the orientation of the image plane in the patient coordinate system.
Most commonly (for CT/MR) this is encoded in the attribute (0020,0037) Image Orientation Patient which contains 6 floating point numbers describing the x,y,z components of the row and column vector of the image.
Please note that this orientation refers to the other slices of the same scan, there is no absolute reference coordinate system.
If this attribute is missing, (0020,0020) Patient Orientation may give you a hint, but not as precisely as the vectors.
I am really confuse over the draw overlay
on MRI Image means its part is similar to Structure Report(SR) Processing or not
I am trying to read the MRI File in such way that from Contrast Agent. Also after so much searching on Google finally get some information such as
"The data is extracted by injecting a contrast agent into a patient’s vein,then taking sequential snapshots of a volume of interest as the contrast agent diffuses through that area"
but i am totally new for this to help out can you help me for
1. Give me specific link for these topic
2. How to read the Contrast Agent value from MRI Dicom File.
3. Also how to show a shaded region where the Cancer is detected or
some kind of marker on that location where the pixel intensity of
dicom file is higher.
Well, MRI scan is just a stack of grayscale images, pretty much as CT is, except that intensity units are of course different. So, just read it as any other dicom image, and look pixels values for intensities, or perform segmentation.
Cancer tumor regions and other features are stored in a separate dicom object, called RT structure set (it is produced usually by radiotherapy planning system or some contouring software).