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 |