AIMS config file

Aims configuration file



Date: 2009/08/26

In AIMS version 2.13 and later, AIMS uses a settings file, currently used to specify SPM IO conventions, and possibly other things in the future. There is one site-wide settings file (in the shared directory of Aims: $AIMS_PATH/shared/aimsrc or $SHFJ_SHARED_PATH/aims/aimsrc) and one personal $HOME/.aimsrc file. Personal settings override site-wide settings. Both files are in the same format: python format at the moment, until we have XML IO. Example:

attributes = {
  '__syntax__' : 'aims_settings', 
  'spm_input_radio_convention' : 1, 
  'spm_input_spm2_normalization' : 0, 
  'spm_output_radio_convention' : 1, 
  'spm_output_spm2_normalization' : 0, 
  'spm_output_4d_volumes' : 0, 
}

By the way, these specific settings correspond to the behaviour of SPM99. They used to be the site-wide defaults in AIMS 3.0 and earlier.
In AIMS 3.1, the defaults correspond to SPM2: all spm_* options set to 1.

Note: these defaults are different from the defaults used by the library if no settings are provided: with no settings provided, AIMS will act like SPM2 does, because it's the future behaviour. Nevertheless many people are still using SPM99, and for smooth compatibility with previous versions of AIMS and Anatomist, we heve decided not to adopt this default right now. When SPM99 has disapeared, we may change the defaults.

Don't change the two first lines: attributes = { is the identifier of the python-like format for the config file, and '__syntax__' : 'aims_settings', identifies the file type to be AIMS configuration file. The other attributes can change, be modified, removed, or added.

The set of currently known attributes (in AIMS 2.13) is:

Attribute name: type: Default value: Explanation: Appeared in AIMS version:
default_writers dictionary { 'Volume' : 'NIFTI1' } Hints about the IO format to use when writing an object with no information about it (no extension, no specified format). The value of this attribute is a dictionary. Each entry key is an object type name, either completely specified ( 'volume of S16'), or a general object type name ('Volume'). The corresponding value is the format name ('NIFTI1', 'GIS' etc.). 3.2
nifti_output_4d_volumes bool 1 Same as spm_output_4d_volumes but for NIFTI-1 format. 3.1
spm_input_radio_convention bool (or at least, number) 1 Determines how to understand the unspecified orientation of SPM images read by AIMS. "Unspecified orientation" means no indication in the .minf file written by AIMS or Anatomist with the image. This flag is quite equivalent to the SPM flag. 0 means neurological convention, and 1 means radiological convention (left and right are flipped). Note that this flag is not supposed to tell Anatomist how to display the image, but how to read it: if read in the correct orientation, Anatomist should always display images in radiological convention by default (unless a display-only flag is set in Anatomist). This flag actually affects processings, but Anatomist flag does not.
When AIMS (or Anatomist) writes an image in SPM format, its orientation convention is written with it in the .minf file going with it.
See this page for further explanations of the SPM format ambiguity.
2.13
spm_input_spm2_normalization bool 1 Determines if normailzed SPM volumes with no specified orientation should be read in SPM99 or SPM2 way.
SPM99 always wrote normalized images in neurological convention, regardless of the input convention.
SPM2 writes norlalized images in the orientation specified for reading, ie if images are specified to be in radiological convention before normalization, the normalized images made from them will be saved in radiological orientation.
See this page for further explanations of the SPM format ambiguity.
2.13
spm_output_4d_volumes bool 1 Allows or forbids 4D volumes writing in SPM format. If disabled, a 4D volume will be split into a series of 3D volumes like SPM99 does. This was the behaviour of previous AIMS releases (2.12 and earlier). See here for further explanations. 2.13
spm_output_radio_convention bool 1 Tells in which orientation images with unspecified orientation should be written to disk in SPM format by AIMS and Anatomist. This flag is especially useful when converting images from another format to SPM format. If images were read already in SPM format, their orientation has been determined at read-time and will not change, so this flag will not apply (unless spm_force_output_convention is set).
See this page for further explanations of the SPM format ambiguity.
2.13
spm_output_spm2_normalization bool 1 Tells if images that are recognized to be normalized should be writen in SPM format preferably in SPM99 or SPM2 convention. If images were read in SPM format, their orientation has already be set at read-time and will not change, so this flag will not act (unless spm_force_output_convention is set).
See this page for further explanations of the SPM format ambiguity.
2.13
spm_force_output_convention bool 0 If set, this flag tells AIMS to override SPM reading orientation when re-writing an image in SPM format, and to force using spm_output_radio_convention and spm_output_spm2_normalization settings. For instance if an image has been determined to be in radiological orientation at read-time, and if spm_force_output_convention is set to 1 and spm_output_radio_convention set to 0, then it will be re-written in neurological orientation.
See this page for further explanations of the SPM format ambiguity.
2.13