Table of Contents
Loading and displaying are two different actions in Anatomist. Loading is reading data stored in memory. While displaying is visualizing the object in Anatomist windows, with maybe modifications. For example, you can load data written in radiological convention and display it in neurological convention. The display options doesn't change data on disk.
Axis in Anatomist are oriented like this :
X axis : right => left
Y axis : anterior => posterior
Z axis : top => bottom
T axis : 4th dimension to visualize a volume with an adding cursor to move from volume to volume ; This axis can stand for the time in functional volumes vizualisation or directions for a diffusion sequence.
When loading a volume, data organisation is supposed to match axis organisation describe before. That is to say data is supposed to be in radiological convention. In this case, data is not modified for displaying in radiological convention.
For volumes in ANALYZE format, reading and displaying data depends on the following properties (attributes in .minf file and .aimsrc configuration file) :
If spm_radio_convention attribute value is 1, data in ANALYZE format is in radiological convention on disk. Else, if spm_radio_convention value is 0, data is in neurological convention.
The following explanations are valid only if your site / station is configured as ours according to the flip parameter of SPM99. So for us, non normalized volumes are in radiological convention and volumes nomralized by SPM99 are in neurological convention. That's why volumes identified as normalized volumes (according to their size in mm) are automatically flipped, to have a coherent display with data in radiological convention.
To go on working in SPM99 mode, your .aimsrc file must be configured like this :
attributes = {
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 0,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 0,
}
Volumes in analyze format are read in radiological convention ('spm_input_radio_convention' : 1) and normalized volumes in neurological convention ('spm_input_spm2_normalization' : 0).
Reading normalized volumes in SPM99 mode
As it is said before, in SPM99 mode, Aims tests the volume dimensions to see if it is normlized or not. A volume is considered as a normalized volume if its dimensions in mm are 152 < x < 165, 185 < y < 195, 130 < z < 145 or 178 < x < 185, 215 < y < 220, 178 < z < 185. In this case, the volume is supposed to be in neurological convention and it is automatically flipped at loading to display it in radiological convention.
It is different for volumes normalized with SPM2. Indeed, there is a parameter defaults.analyze.flip which indicates if input data must be flipped. (for more details, see SPM2 documentation). So data normalized with SPM2 can be either in radiological convention or in neurological convention. The aim is to keep the same convention for input and output data (before and after normalization).
To work in SPM2 mode (input convention = output convention), your .aimsrc file must be configured like this if your data is in radiological convention :
attributes = {
'__syntax__' : 'aims_settings',
'spm_input_radio_convention' : 1,
'spm_input_spm2_normalization' : 1,
'spm_output_radio_convention' : 1,
'spm_output_spm2_normalization' : 1,
}
Anatomist needs to manage displaying like this because there isn't reliable information to indicate the convention. Some header attributes have this information but it can be incorrect or out of date. For example, SPM2 doesn't rewrite the header of modified volumes.
The origin of volumes is the voxel whose coordinates are (0, 0, 0). This voxel is located forward, on top and on the right of the volume. So, in an axial Anatomist window, this point will be at the top left corner if you keep the radiological display mode. If the origin is in mm, the origin of the volume is the centre of the voxel located at the origin.