Why objects and windows are not always in the same referential ? | |
Each object and window has its own referentials, they're independant and can be different. If an object and window have different referentials and a transformation between the two referentials exists, the transformation is applied to the object in order to visualize it in the window's referential. If the transformation doesn't exist, no transformation is applied to the object and it is exactly as if the object and the window had the same referential. | |
How to create a transformation ? | |
There are several ways :
Using Aims commands to register 2 volumes (AimsMIRegister and AimsManualRegistration). Using Anatomist transformation control in order to do a manual registration. Convert .mat files into .trm files with BrainVISA processes :
fMRI => converters => SPM to AIMS transformation converter and
fMRI => converters => SPM sn3d to AIMS transformation converter. These processes need a Matlab licence. Only affine part of the transformation is converted. You can write your own transformation file. | |
How to reorient an image if sagittal view is inverted ? | |
You can use the commands AimsFlip or VipFlip in order to invert axis X, Y or Z. | |
What is the difference between superimposing and merging images ? | |
A fusion creates a new object. There are several types of fusion : 2 volumes, a texture and a mesh... Superimposing object also enables to visualize several objects at the same but it doesn't create a new object. Whereas a fusion is a new object which has its own properties. | |
Is it possible to normalize with Anatomist ? | |
The only way would be to load a transformation to put an object in a known referential. | |
What is the difference between loaded and displayed images in Anatomist ? | |
Loading an image doesn't modify it whereas it can be modified for display. For example, your loaded image is in radiological mode but you configured 'Display in neurological mode', so the image is modified only for display, but not on disk. | |
Why talking about objects rather than images ? | |
Because Anatomist enables to visualize several types of objects, not only images. For example, a graph is not really an image but a structured object with nodes and attributes. | |
How to obtain series of Analyze 3D images rather than Analyze 4D images ? | |
Set the field 'spm_output_4d_volumes' to 0 in configuration file .aimsrc. | |
Why do I see a gap when I merge 2 normalized volumes ? | |
Indeed, Anatomist and SPM doesn't manage referentials in the same way. Particularly, it is not the same voxel that is considered as the origin of the volume. But information about referentials, transformations is generally written in the file header and Anatomist can read this information and load the corresponding referentials and transformations. To do that, use the menu Referential -> Load information from file header. | |
Why the origin of my volume (0,0,0) is located in the top right corner ? | |
Indeed, in Anatomist, the voxel (0,0,0), the origin of the volume is located at the front top left corner of the volume's box. If you see, this point on the right, it is because your are in radiological mode, so the left and right are inverted in display. | |
How to save a graph node (ROI, sulcus ...) into a volume ? | |
Load the graph, select the node and right-click on it. Then choose 'File' -> 'Export mask as volume'. | |
How to zoom, translate and rotate a volume ? | |
Use Anatomist default control. To know the available keyboard shortcuts, pass the mouse on the control's icon. | |
Why a graph isn't visible when I put it in a 3D window ? | |
By default, the graph nodes are not displayed because it can be heavy and not clear if there are a lot of nodes. You have to choose the node you want to see by selecting them. But it is also possible to ask for displaying all the node in graph display menu. See the section Handling a graph. | |
How to know software version (Aims, BrainVISA and Anatomist) ? | |
You can run an Aims command with --version option, for example AimsFileInfo --version. You can also read the version number at the top of Brainvisa and Anatomist interface.. | |
How to know the volume of a region ? | |
There are 2 ways :
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When I put a volume in a window, I don't see the volume. | |
Check that the window is in a mode : axial, coronal or sagittal. Indeed, if the window is a 3D window, you have to rotate the volume. By default it is not visible. To rotate, use the middle mouse button and move the mouse. | |
How to draw a ROI on the 3 views at the same time ? | |
Check that the option LinkedCursor is enable in the Paint tab of the ROI toolbox and open all views (axial, coronal, sagittal et 3D) via Painting views in ROI management tab. | |
Can I draw on a fusion ? | |
No, this feature is not yet available. | |
Is it possible to draw a ROI on a mesh with Anatomist ? | |
Yes, it is possible since 4.1 version. Please, see Surface paint module. |